. You simply load your trajectory > into VMDReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. From: Gianluca Interlandi (gianluca_at_u. washington. Rooms and beds. washington. washington. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. > > Gianluca >Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Bedrooms: 1 (People: 2) Bedroom 1. In the NAMD folder that you downloaded there >> is a file called "notes. edu> wrote: > I'm cc'ing here the NAMD list so that others. I would be > happy if somebody could point me out to some scripts which help me performRe: Help building a desktop for namd. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. washington. uiuc. I wanted to briefly update here on my > experience. >Re: Vibrational mode analysis. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. washington. washington. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. I needed to install the 'patch' program. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). edu: "Re: high (or low) pressure readings" Next in thread: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Brian Bennion: "Re: fatal error"> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. > > According to your banchmarks, it looks like the less expensive GTX285. On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Pavel Aprikian, # 1 Gianluca Interlandi, # 2 Brian A. washington. > > I have already run a bunch of pulling simulations in the NVE ensemble. I needed to install the 'patch' program. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. The difference is usually after the > 4th decimal after the period. > > Gianluca > > On Wed, 23 Sep 2015, John Stone. Gianluca has 2 jobs listed on their profile. washington. washington. edu> > wrote:Re: Help building a desktop for namd. At some point there will be a web page here. Biochemistry. edu> wrote:Gianluca Interlandi. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. 7 ns/day, which seems decent given the system size. PMID: 33550613 PMCID: PMC8089038 DOI: 10. 7 released. It's > slightly faster but still not that much faster than running on 16 CPU cores. From: Mitchell Gleed (aliigleed16_at_gmail. Proteins. washington. running multicore version on a 2-CPU node. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. I'm testing specifically this protein for its beaviour. 7b1 on NCSA Abe. In the text > field you can enter your atom selection, e. 85. Don't take my word that this works. washington. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. edu> wrote: > Hi Fatemeh, > > Thanks for replying. 7b1 - effects of configuration parameters and hardware. edu> > wrote:Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. From: Gianluca Interlandi (gianluca_at_u. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. washington. From: Victor (ovchinnv_at_gmx. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. washington. Eric Klavins Professor. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. I also ran a non-CUDA job on Forge > using 16 CPUs. From: Gianluca Interlandi <gianluca_at_u. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. I was getting 2. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. edu) Date: Wed Dec 12 2012 - 14:49:46 CST Next message: JC Gumbart: "Re: NAMD and new FF CHARMM36" Previous message: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" In reply to: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" Next in thread: Jeffrey Potoff: "Re: NAMD and new FF CHARMM36" > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. Facilities. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. You should simulateCorresponding Author. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. I made those videos seven years ago. C; the more troublesome part is the lack of long-range electrostatic treatments. edu> wrote: > Roy, > > I think that you are confusing two things. J. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. " >> Could a small damping coefficient lead to such errors? If so, what would >> be the scenarioGianluca On Sun, 30 Aug 2009, Axel Kohlmeyer wrote: > On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: >> Thank you Mike for sharing your information. washington. at 298. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. edu. NAMD doesn't that i know of. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu> wrote: > Dear all, > > Does anybody have experience simulating carbohydrates with NAMD? In > particular, I'm interested whether the CHARMM or the AMBER force field is > more accurate to simulate carbohydrates. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. 478 KJ/mol = 0. Hope the video helps, but now I'm embarrassed. washington. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. washington. edu) Date: Sat Jul 04 2015 - 15:33:25 CDT Next message: VINAYAK BHAT: "Generating solvent models. uiuc. In this way, you could get a feeling what NAMD can do before you > invest money. SMD on center of mass. From: Stern, Julie (jvstern_at_bnl. From: Gianluca Interlandi (gianluca_at_u. Kidd, 2 Isolde Le Trong, 3 Veronika Tchesnokova, 1 Olga Yakovenko, 2 Matt J. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Entertainment. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. Cancellation policy. washington. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. m. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. 97 pN*nm = 1 Kcal/molOn Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote: > Dear vmd list, > > I noticed that I get slightly different results when I measure the > distance between two atoms using "measure bond" vs by measuring the length > of the vector between the two atoms. Just source the Tcl file and use the 'unwrap' procedure. I > > attach a plot of a constant velocity simulation where I'm pulling twoRe: NAMD 2. 7 released" In reply to: Jim Phillips: "Re: NAMD 2. Michel Espinoza-Fonseca: "Re: Vibrational. edu> wrote: > Hi Fatemeh, > > Thanks for replying. What are you trying to accomplish?Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a jsLe mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. washington. VMD-L Mailing List. 7b1 on NCSA Abe. From: Gianluca Interlandi (gianluca_at_u. Gianluca Interlandi. edu> > wrote: > Roy, > > I think that you are confusing two things. Rachel Klevit WRF Endowed Chair in Biochemistry. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. On Thu, Oct 20, 2011 at 05:48:32PM -0700, Gianluca Interlandi wrote: > Dear VMD users, > > A while ago I bothered this list asking for recommendations for a > lightweight laptop to buy which would support a decent 3D acceleration in > order to use VMD in presentations. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorGianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by. Re: replica exchange and GPU acceleration. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. 10. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Michel Espinoza-Fonseca: "Re: Vibrational. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Re: NAMD 2. Both > simulations were started from X-ray structures. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. uiuc. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. washington. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. From: Gianluca Interlandi (gianluca_at_u. washington. > > gianluca, >Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. edu> Cc: <namd-l_at_ks. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. From: Mitchell Gleed (aliigleed16_at_gmail. Interlandi et al. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. washington. washington. washington. g. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ attachment ] If that's the only force you are applying to the system, then that is your external work. edu> > wrote: > are other people also using those GPUs? > > Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] This archive was generated by Research Assistant Professor gianluca@u. (Oct-Nov 1997) Spanish: Fluent written and spoken German: Basic Knowledge WORK EXPERIENCE 2019 October: Founder Host. I doubt that there is a way to have NAMD output theFrom: Gianluca Interlandi (gianluca_at_u. 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. washington. uiuc. washington. Gianluca Interlandi , Contributed equally to this work with: Pavel Aprikian, Gianluca Interlandi Affiliation Department of Bioengineering, University of Washington, Seattle, Washington, United. There have been over 180 downloads and no complaints so far. Biochemistry. I know the lack of treatment of the hydrophobic part but the point here is the different results for same implicit solvent model. From: Gianluca Interlandi (gianluca_at_u. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Electrical. From: Gianluca Interlandi (gianluca_at_u. com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. washington. From: Gianluca Interlandi (gianluca_at_u. washington. I would like to erase Windows and install Leap 42. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. washington. edu on behalf of Gianluca Interlandi [gianluca_at_u. edu> > wrote: > Roy, > > I think that you are confusing two things. washington. Semantic Scholar's Logo. From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. washington. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. Write a review. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. PMID: 37700555; DOI: 10. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. Neil King Assistant Professor. washington. coli UTI89 on mannan-coated surfaces and bladder infection in mice. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. The simulations were not performed at constant velocity > but at constant force. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated lectin domain (LD) that binds mannose on the. Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. washington. washington. washington. I was recording the energies once every 100 steps. washington. Stenkamp, 3 Wendy E. From: Gianluca Interlandi (gianluca_at_u. I made those videos seven years ago. From: Gianluca Interlandi (gianluca_at_u. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. washington. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote: > Dear list, > > Starting with version 1. edu> > wrote: > are other people also using those GPUs? > > From: Gianluca Interlandi (gianluca_at_u. washington. Spaces. >> >> i am attaching some graphs with performance numbers from. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. From: Gianluca Interlandi (gianluca_at_u. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Deadline is this Friday (or in three > months). washington. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. Gianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. >From: Gianluca Interlandi (gianluca_at_u. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. >From: Gianluca Interlandi (gianluca_at_u. washington. Stereo system. washington. 15 K 1 KT = 2. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Sarah Keller Professor. washington. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. washington. Corresponding Author:gianluca@u. rtf" and "par_all36_prot. 15 K 1 KT = 2. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. Sokurenko 1 , *. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. washington. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. washington. washington. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. <br> <br>1999 March: Degree in modern languages result 107/110 - University of Catania, Italy with a degree thesis on Irish. 26588. 1. 1002/prot. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. Comparative controls consisted of FocH (high affinity with and. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. , and Thomas W. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. washington. In reply to: Gianluca Interlandi: "Compiling NAMD 2. From: Gianluca Interlandi (gianluca_at_u. Next in thread: Gianluca Interlandi: "Re: NAMD 2. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. Hemostasis in vertebrates involves both a cellular and a protein component. Gianluca Interlandi. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. I am > using the option "wrapAll on". From: Victor Kwan (vkwan8_at_uwo. unam. washington. Sarah Keller Professor. From: Gianluca Interlandi (gianluca_at_u. I doubt that there is a way to have> On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi > <gianluca_at_u. But if you simulate entire proteins, charged termini. Gianluca has 2 jobs listed on their profile. washington. Cancellation policy. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you canThe bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. washington. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. > However, topology and parameters for water and ions are. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. Biochemistry. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. Academic ProgramsFrom: Gianluca Interlandi (gianluca_at_u. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? Next in thread: Gianluca Interlandi: "Re: NAMD 2. 1002/prot. washington. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. From: Gianluca Interlandi (gianluca_at_u. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. washington. Try copying it again from where the simulation was run. From: Gianluca Interlandi (gianluca_at_u. washington. washington. My> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. washington. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. 7 with the PLUMED patch" Previous message: Alex Liu: "Fix atoms-Colvars" Next in thread: Gianluca Interlandi: "Re:. washington. I'm testing specifically this protein for its beaviour. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. View the profiles of people named Gianluca Interlandi. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Forest, Academic Editor. washington. uiuc. washington. washington. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. Just source the Tcl file and use the 'unwrap' procedure. View all 11 amenities. Display options. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. Specifically, I’m testing different binding domains. Previous message: Gianluca Interlandi: "NAMD 2. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. From: Gianluca Interlandi [gianluca_at_u. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. 100% refund of amount payable if you cancel at least 14 days before check-in. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. I'm > not sure whether the CHARMM program can read. washington. uiuc. From: Gianluca Interlandi (gianluca_at_u. On Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). Interlandi G. washington. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. edu) Date: Thu Apr 05 2012 - 15:44:43 CDT Next message: Gianluca Interlandi: "Re: DCD" Previous message: Jérôme Hénin: "Re: changing harmonic restraints (colvars)" Next in thread: Gianluca Interlandi: "Re: DCD" Reply: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ].