Re: [gmx-users] single precision to double precision version
On Tue, Oct 9, 2012 at 12:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/9/12 12:21 PM, Ali Alizadeh wrote: Dear All users How to convert my single precision version of gromacs to double precision? Is it possible? You don't; you re-install Gromacs with the desired precision. Note that single- and double-precision installations can exist side-by-side with proper suffixes (default _d) on the executables and libraries. Can i do it by apt get command in ubuntu version? It looks to me like the only version available is single-precision but perhaps someone else who uses them regularly can tell. I do all my installations from source. -Justin The gromacs packages that come with Ubuntu contain both single and double-precision binaries, with the latter ones having the usual _d suffix. I have checked that on Ubuntu 10.04 Lucid Lynx (gromacs 4.0.7) and Ubuntu 12.04 Precise Pangolin (gromacs 4.5.5). Oliver -- $ g_luck_d -c :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_luck_d (double precision) (-: gcq#91: I Can't Shake It (Dinosaur Jr) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force constant - units
Hi Steven, How much is 1 [pN/A] in [kJ/nm2] (without the mol)? And why would anyone want to use force-constants in the 10^-23 ? So why not define a force-constant for 1 mol of bonds instead of a sole bond? I think you can see where I'm going. Oliver On Fri, Jun 29, 2012 at 2:32 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, How to recalculate the force constant from the harmonic potential: 1 [pN/A] into [kJ/mol nm2] ? Where is the [mol] here? Thanks, Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] movement in 2 directions - remove one degree of freedom
Hi, as an alternative of applying position restraints to only the y-component, one can also define a freeze-group only to act on the Y-axis by using: freezedim N Y N see: http://manual.gromacs.org/online/mdp_opt.html#neq freezegrps and freezedim Oliver On Fri, May 11, 2012 at 7:39 AM, Erik Marklund er...@xray.bmc.uu.se wrote: 11 maj 2012 kl. 14.38 skrev Steven Neumann: Dear Gromacs Users, Is there any way in Gromacs which will allow me to contraint some of the atoms in the system to move only in the coordinate X and Z? I do not want some of my atoms to move in Y direction. Do you know how to do this? Hi, Not exactly. But you can apply position restraints with zero force constants in X and Z directions. This will allow some movement in the Y direction, but the extent depends on your force constant in the Y direction. Erik Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] some hardware questions
Hi all, This week Nvidia has also announced the GeForce GTX 690 with two Kepler Chips [1]. That will make a total of 3072 CUDA cores @ 915MHz to 1019MHz and will perform like two GTX 680s in SLI mode [2], but more energy efficient. I'd really be interested if parallelization would be a bottleneck for the Kepler chips compared to the Fermi ones. Has anyone already run some benchmarks on Kepler? Best, Oliver [1] http://nvidianews.nvidia.com/Releases/NVIDIA-Unveils-GeForce-GTX-690-Dual-Graphics-Card-Combines-World-s-Fastest-Gaming-Performance-With-Sleek-Sexy-Design-7c1.aspx [2] http://www.geforce.com/whats-new/articles/article-keynote/ On Wed, May 2, 2012 at 10:16 AM, Peter C. Lai p...@uab.edu wrote: On 2012-05-02 06:13:04PM +0200, Mirco Wahab wrote: Hello Peter, Am 02.05.2012 17:44, schrieb Peter C. Lai: You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx 680) in it. That should max the performance. asm is pretty much stagnant for general purpose procs since core2 came out. Is this true? To my knowledge, the Fermi GPU (GF-110, eg. GTX-580) is a 16 processor (streaming multiprocessor, SM) system, each processor having 32 cores running at 1.5 GHz, and the Kepler-1 (GK-104, eg. GTX-680) an 8 processor system with 192 cores per processor at 1GHz. Because on the Fermi each SM has more L1 cache than each SM on the Kepler-1 and because it might be harder to saturate 192 cores in a compute-scenario, I'd expect the 580 (GF-110) to be significant(?) faster in the next Gromacs (4.6). Maybe somebody tested this already. (Here in Germany, I can by GTX-580/3GB for ~325€ + Tax.) Regards, M. You might be. I do have a collaborator in France who chooses to use GTX 580 with NAMD and is eschewing the Keplers. I think I saw a bench somewhere for Kepler compute; not sure if I saw that much difference (but you will be paying the price though). In that case stick with Fermis for now :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] large scale simulation?
Hi Albert, With the Information you give here, it's hard to give you specific advice on how to speed up your simulations. I found the following papers quite interesting and maybe they give you some idea in how to improve the performance. 1. Larsson P, Hess B, Lindahl E (2011) Algorithm improvements for molecular dynamics simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science 1: 93-108. Available: http://doi.wiley.com/10.1002/wcms.3 2. Larsson P, Lindahl E (2010) A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescaling. Journal of Computational Chemistry 31: 2593-600. Available: http://dx.doi.org/10.1002/jcc.21552 3. Bjelkmar P, Larsson P, Cuendet MA, Hess B, Lindahl E (2010) Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. Journal of Chemical Theory and Computation 6: 459-466. Available: http://pubs.acs.org/doi/abs/10.1021/ct900549r On Fri, Mar 30, 2012 at 11:02, Albert mailmd2...@gmail.com wrote: Hello: I am wondering does anybody have experience with GROMACS for large scale simulation? I've heard lot of people said that it would be difficult for Gromacs to do so. eg: I've got a 60,000 atoms system, is it possible for GROMACS to produce 100 ns/days or even more? suppose I can use as much CPU as possible My recent experience for such system, Gromacs can only produce up to 20ns/day If I would like to produce 1000 ns, I have to wait for 50 days.. thank you very much best A. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Where would I find the 45A4 GROMOS force field?
Hi Marc, Though I never came across ready-to-use files for Gromos 45A4, you can for sure get all the parameters for carbohydrates from [1] and transfer them into a Gromacs format (make sure to convert all the units). Searching briefly for the term 45A4 in [2] lets me believe, that the parameters have been cooperated into 53A5 and 53A6, so you might want to check that as well. [1] Lins RD, Hunenberger PH (2005) A new GROMOS force field for hexopyranose-based carbohydrates. Journal of Computational Chemistry 26: 1400-1412. Available: http://dx.doi.org/10.1002/jcc.20275. [2] Oostenbrink C, Villa A, Mark AE, Gunsteren WF van (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry 25: 1656-76. Available: http://dx.doi.org/10.1002/jcc.20090. Oliver On Wed, Mar 28, 2012 at 07:28, Marc Gordon marcgrd...@gmail.com wrote: Ah well no worries. I will delve back into the gromacs and NAMD user guides and see what I can dig up with regards to getting these GROMOS files working through NAMD. Thanks again for the help you have given me. Marc On Wed, Mar 28, 2012 at 4:19 PM, Justin A. Lemkul jalem...@vt.edu wrote: Marc Gordon wrote: Oh awesome. Thanks so much for this. I've never worked with GROMOS or gromacs themselves. I'm going to need to look up whether or not it is possible to use these files to generate files in the gromacs format required as input for NAMD now but at least having access to the force fields puts me that much further along. I don't suppose you know offhand whether such a thing is possible? Sorry, but I don't. I haven't done anything with NAMD that wasn't out of the box. That's probably a question better posed to the NAMD people. -Justin I see they have a myriad of force fields available on ATB including the other one I am interested in 53A6. Thanks again. On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Marc Gordon wrote: Hi all I have never posted to the mailing list before but it has proven very helpful in the past. I'm looking for the 45A4 force field. I've been asking Mr. Google but so far I haven't had any luck locating it. This is I imagine probably down to the wrong keywords or something I want to do some work on disaccharides and I would very much like to use this force field. I'm going to be using it thorugh NAMD. I thought this would be the best place to ask if anyone knew of a site where this force field was being maintained or something. You can get the files from ATB: http://compbio.biosci.uq.edu.__au/atb/ http://compbio.biosci.uq.edu.au/atb/ They are formatted for use with the GROMOS MD package, but that's the only source of these files of which I'm aware. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Neigborsearching, Electrostatics and vdw options
Hi Ahmet, Let's imagine a sphere(two concentric spheres): radius of the inside small sphere=rvdw radius of the big sphere=rcoulomb distance between two of our nested spheres:rlist is this approach correct? No. I suggest you read section 4.6.3 (and probably also 4.6.2) in the Gromacs Manual. The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone for the fact that the neighbor-lists are only updated every nstlist steps (often nstlist = 5). Oliver 2012/3/21 ahmet yıldırım ahmedo...@gmail.com: Dear users, Berk Hess says: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Mon Jul 16 14:17:12 CEST 2007 There are three options in Gromacs. The option you want is rcoulomb rlist and rvdw rlist. This works and gives the most accurate and also the most costly integration. A faster and very commonly used setting is: rlist=rcoulomb=rvdw. With PME the Coulomb interactions are very small at the cut-off, as are the LJ interactions. So with a small sacrifice in integration accuracy one can gain a lot of performance, also because analytical LJ is cheaper than tabulated. The last option is rcoulomb rlist and/or rvdw rlist. Then the energies and forces beyond rlist are only updated every nslist steps. This gives less integration accuracy but can give a lot of interaction accuracy at a small computational cost. Justin A. Lemkul says: [gmx-users] Twin-range cut-off Tue Sep 13 01:25:28 CEST 2011 A twin-range cutoff just means that your short-range cutoffs aren't all the same value, such that they form two interaction zones. Within the shortest, the neighbor list is updated every step. Between the shortest and longest cutoffs, the neighbor list is updated every nstlist steps. For instance: rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 are common settings for Gromos96 force fields (in conjunction with PME). Thus there are two interaction zones - the first is if two atoms (or charge groups, depending on the algorithm) are within 0.9 nm, and the second is if the two interacting species are beyond 0.9 nm but within 1.4 nm of each other. rcoulomb: distance for Coulomb cut-off (nm) rvdw:distance for LJ or Buckingham cut-off (nm) nstlist: neighbor list update frequency rlist: cut-off distance of the short-range neighbor Twin range cutoff consists of rcoulomb and rvdw, isnt it? Let's imagine a sphere(two concentric spheres): radius of the inside small sphere=rvdw radius of the big sphere=rcoulomb distance between two of our nested spheres:rlist is this approach correct? I could not understand the fourierspacing and rlist. Thanks in advance 21 Mart 2012 20:53 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: Dear users, I have two configuration as the following related to Neigborsearching, Electrostatics and vdw options. I checked the literature: Generally the rlist, rcoulomb and rvdw have used as the following. rlist=1 rcoulomb=0.8 rvdw=1.4 Is there much difference between the following two options in the calculation/the results? Is there one significant difference between the two options. If yes, then what is it? What is relationship between rlist, nstlist and rvdw/rcoulomb? Furthermore, fourierspacing = 0.16 or fourierspacing = 0.12 difference between these two options? 1.choice . ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order = 4 fourierspacing = 0.16 rcoulomb = 1.0 vdw-type = Cut-off rvdw = 1.0 ... 2.choice .. ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order = 4 fourierspacing = 0.16 rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 ... Thanks in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb file
A neat way to get generic coordinates of organic molecules like this is using Jmol: 1) go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?USESIGNED This requires Sun/Oracle Java plugin activated in the browser and asks for permission to trust the signed applet. Alternatively one could use the Jmol Application instead. 2) type the following two commands into the cmd textbox (or the Jmol console) load $Thiophene ; write coords ? ; The first one will load the structure and the second one will open a Save-File dialog to ask for the filename to save it on your hard disk. Quoting Bob Hanson (currently the lead Jmol developer): If you can name it [and if it is organic] [...] you can probably get it. Cheers, Oliver On Mon, Mar 12, 2012 at 12:42, dina dusti dinadu...@yahoo.com wrote: Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 12, 2012 10:02 PM Subject: Re: [gmx-users] pdb file dina dusti wrote: Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? There are numerous methods for producing coordinate files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:g_energy
Hi Stephan,
Have a look at:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
something like this should work:
--8--schnipp--8--
#!/bin/bash
for i in Temperature Pressure ; do
g_energy -f ener.edr -o ${i}.xvg EOF
${i}
EOF
done
--8--schnapp--8--
creating Temperature.xvg and Pressure.xvg assuming there are terms
named like this in your ener.edr file.
The braces around the i might not be necessary in this case, but don't
hurt either.
Best,
Oliver
On Fri, Mar 9, 2012 at 08:00, lloyd riggs lloyd.ri...@gmx.ch wrote:
Dear All,
Is there a way to either supress the interactive portion of g_energy and
print out everything listed, or pass it to something more automated? MY
problem, I spent an hour or three trying to just write an automated four line
shell or python script to extract all the terms listed based on index files.
The error comes as I can not pass a variable i once the interactive portion
of the g_energy is invoked (I get error $i, i '$i', $i, etc.. does not
match a pattern or whatever as an error each time). Basically try getting a
few dozen terms from an energy file, times 20 to 100 necessary runs...
Sincerely,
Stephan Lloyd Watkins
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: How to use Inflategro with different lipid types
Hi, I recently came across the CELLmicrocosmos 2.2 MembraneEditor, in which one can easily generate coordinates for mixed membranes and AFAIK also insert a protein. http://cm2.cellmicrocosmos.org/ http://pubs.acs.org/doi/abs/10.1021/ci1003619 I haven't had the chance/need to actually try it, though. Cheers, Oliver 2011/5/2 Ioannis Beis ib...@mail.student.oulu.fi: Hello, I would like to thank Justin and Tom for their kind replies to my question! I believe that by having the gromacs manual as a guide I would manage to bring the bilayer into physiological size by using Justin's advice. However, Tom's advice sounds simpler to implement. Unfortunately the size of the pre-equilibrated POPC is too small for what I want to do afterwards, but I can make my own POPC using editconf, genconf and Inflategro to shrink and equilibrate it first and then use the renaming trick. For beginner users that will consult this thread in the future, I had overestimated the value of the coordinate files as starting structures... Deleting the last two united atoms from oleoyl will fix the hydrocarbon chain length and using a palmitoyl force field will take care of turning the double bond into a single one. Renaming the three different united atoms' names in the polar heads and eventually the names of the whole lipids is like turning ethanolamine into choline and vice versa. The initial positions at the crucial points will be very improper, but this isn't important since hopefully the energy minimization will fix them. This strategy -with a little more work- could even be applied for more diverse polar heads as soon as one has a force field, just by placing his atoms at very reasonable initial positions! Proper topology file is all that matters :). Thanks again for your ideas! Yiannis -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x manual
Dear Gromacs Community, as I understand the MDP option continuation is the new name for the option unconstrained_start. I think the 4.5 series manual should be updated to mention that fact, since it still only mentions unconstrained_start (at least the html version of gromacs 4.5.1 : /usr/local/gromacs-4.5.1/share/gromacs/html/online/mdp_opt.html#bond ) although that name seems to be deprecated since Gromacs 4.0. Oliver -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Inconsistent charges in OPLS-AA residues ASPH and GLUH
Hi, while having a closer look at the topologies of aspartic- and glutamic-acid in OPLS-AA, I noticed that the charges of the carboxylic oxygen atoms are not consistent in the protonated forms of those residues: from ffoplsaa.rtp of gromacs 4.0.7: [ ASPH ] [ atoms ] Nopls_238 -0.500 0 Hopls_2410.300 0 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_136 -0.120 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_2670.520 3 *OD1*opls_269 *-0.530* 3 *OD2*opls_268 *-0.440* 4 HD2opls_2700.450 4 Copls_2350.500 5 Oopls_236 -0.500 5 [ ... ] [ GLUH ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_136 -0.120 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_136 -0.120 3 HG1opls_1400.060 3 HG2opls_1400.060 3 CDopls_2670.520 4 *OE1*opls_269 *-0.440* 4 *OE2*opls_268 *-0.530* 5 HE2opls_2700.450 5 Copls_2350.500 6 Oopls_236 -0.500 6 in case of ASPH atom OD1 has a charge of -0.530 while it's equivalent in GLUH (OE1) has a charge of -0.440 and vice versa for OD2 and OE2. While fast browsing over the OPLS-AA papers, I couldn't find a listing of the original charges to confirm which of the cases is the correct one. For all other forcefields for gromacs that have topologies for the protonated forms of aspartic- and glutamic-acid (gromos, ffencads and charmm27.ff (in GMX 4.5) the charges of OD1 and OD2 in ASPH match to the corresponding ones in GLUH. I found this in the ffoplsaa.rtp of gromacs 4.0.7 and as far as I can see it's currently the same in the branches release-4-0-patches and release-4-5-patches. Cheers, Oliver -- Oliver Stueker NRC - National Institute for Nanotechnology / University of Alberta, Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs, lam and condor
Hi Hsin-Lin,
As Mark answered already yesterday:
1) 1Gb Ethernet is not fast enough for more than 2 or maximum 4 CPUs.
(and if each process of mdrun has to wait ~90% of the time to get data
from the others, then you result in just 10% load, right? )
2) telling from the line:
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
you are using a double precision of gromacs that slows things down and
is only of use in very special cases. use mdrun_mpi instead.
3) your system is just 6000 atoms small, I would rather run such a
small system on one dual-core system (so max 2 CPU's)
I don't think the system will scale well on more CPU's
And in case there's really something wrong with condor and has nothing
to do with gromacs then this is the wrong mailing-list anyway.
Oliver
2010/4/4 Hsin-Lin Chiang jian...@phys.sinica.edu.tw:
Hi,
I tried to use 4 and 8 CPUs.
There are about 6000 atoms in my system.
The interconnect of our computer is the network with speed 1Gb but not
optical fiber.
I'm sorry for my poor English and I couldn't express well in my question.
Everytime I submitted the parallel job, the nodes assigned to mehave been
100% loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable script,
and I post them in my previous message.
How should I correct my script?
Hsin-Lin
Hi,
how many CPUs do you try to use? How big is your system. What kind of
interconnect? Since you use condor probably some pretty slow interconnect.
Than you can't aspect it to work on many CPUs. If you want to use many
CPUs
for MD you need a faster interconnect.
Roland
2010/4/2 Hsin-Lin Chiang jian...@phys.sinica.edu.tw
Hi,
Do someone use gromacs, lam, and condor together here?
I use gromacs with lam/mpi on condor system.
Everytime I submit the parallel job.
I got the node which is occupied before and the performance of each cpu
is
below 10%.
How should I change the script?
Below is one submit script and two executable script.
condor_mpi:
#!/bin/bash
Universe = parallel
Executable = ./lamscript
machine_count = 8
output = md_$(NODE).out
error = md_$(NODE).err
log = md.log
arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
+WantIOProxy = True
should_transfer_files = yes
when_to_transfer_output = on_exit
Queue
---
lamscript:
---
#!/bin/sh
_CONDOR_PROCNO=$_CONDOR_PROCNO
_CONDOR_NPROCS=$_CONDOR_NPROCS
_CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
SSHD_SH=`condor_config_val libexec`
SSHD_SH=$SSHD_SH/sshd.sh
CONDOR_SSH=`condor_config_val libexec`
CONDOR_SSH=$CONDOR_SSH/condor_ssh
# Set this to the bin directory of your lam installation
# This also must be in your .cshrc file, so the remote side
# can find it!
export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
export PATH=${LAMDIR}/bin:${PATH}
export
LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
. $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
# If not the head node, just sleep forever, to let the
# sshds run
if [ $_CONDOR_PROCNO -ne 0 ]
then
wait
sshd_cleanup
exit 0
fi
EXECUTABLE=$1
shift
# the binary is copied but the executable flag is cleared.
# so the script have to take care of this
chmod +x $EXECUTABLE
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
export LAMRSH=$CONDOR_SSH
# when a job is killed by the user, this script will get sigterm
# This script have to catch it and do the cleaning for the
# lam environment
finalize()
{
sshd_cleanup
lamhalt
exit
}
trap finalize TERM
CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
export $CONDOR_CONTACT_FILE
# The second field in the contact file is the machine name
# that condor_ssh knows how to use. Note that this used to
# say sort -n +0 ..., but -n option is now deprecated.
sort $CONDOR_CONTACT_FILE | awk '{print $2}' machines
# start the lam environment
# For older versions of lam you may need to remove the -ssi boot rsh
line
lamboot -ssi boot rsh -ssi rsh_agent $LAMRSH -x machines
if [ $? -ne 0 ]
then
echo lamscript error booting lam
exit 1
fi
mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@
CHILD=$!
TMP=130
while [ $TMP -gt 128 ] ; do
wait $CHILD
TMP=$?;
done
# clean up files
sshd_cleanup
/bin/rm -f machines
# clean up lam
lamhalt
exit $TMP
md.sh
#!/bin/sh
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
-s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \
-e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g
Re: [gmx-users] Re: How to include sodium ion (Reply to Justin's mail)
Hi Lum, (Aside: Can you help with replying emails via this forum. I use gmail and when I click the reply tab, it includes all the mails for that issue, and there is no subject entry. So I always have to copy and paste the mail before replying. I appreciate your help). Even in Gmail you can edit the subject line: Between Add Bcc and Attach a file I have a link called Edit Subject that will open a text-box to do exactly that. Oliver (Sorry if it's a bit off-topic, but maybe it helps that one or the other person to correct the subject-line when replying to the Digest.) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] large number of molecules
Hi Karim, On Mon, Mar 8, 2010 at 18:11, Justin A. Lemkul jalem...@vt.edu wrote: ksm tprk wrote: My mdp file is what http://cs86.com/CNSE/SWNT.htm has. I used nose-hoover for Tcouple. and the beginning of mdp code looks like: Partial information is useless. Post the whole .mdp file; there are plenty of parameters that can be set incorrectly or inconsistently. In addition to Justin, you haven't told us even which forcefield you are using. I hope it's not ffgmx as it is in the reference you gave us. Search the Archive and the Gromacs wiki for reasons not to use ffgmx. Oliver -Justin ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.0005 nsteps = 1000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Angular ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = I used gromacs 3.3.3 and in the vacuum. I applied the heat first around 10 layers. after I finished my simulation and look at the edr file, the result temperatures are higher than what I gave. It looks like it generates heat by it self. But when I do same simulation with less molecules such as 6000, it looks fine. Date: Tue, 9 Mar 2010 08:57:12 +1100 From: dallas.war...@pharm.monash.edu.au Subject: RE: [gmx-users] large number of molecules To: gmx-users@gromacs.org You are going to have to provide a lot more details than that if you want some help. What is “wrong results”? What is your input (copy and paste some commands in)? What is the output (copy and paste)? What makes you think the results are “wrong”? In what situations are they “right”? … and there are a lot more questions that could be asked …… Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *ksm tprk *Sent:* Tuesday, 9 March 2010 8:33 AM *To:* gromacs users *Subject:* [gmx-users] large number of molecules Hello, I simulate carbon nanotube and basically I follow up http://cs86.com/CNSE/SWNT.htm But when I increase the number of molecules (like 15000) , it gives me wrong results. Do you know why this is happen? Thank you, Kasim Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. http://clk.atdmt.com/GBL/go/201469229/direct/01/ Hotmail: Powerful Free email with security by Microsoft. Get it now. http://clk.atdmt.com/GBL/go/201469230/direct/01/ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Oliver Stueker Post-doctoral Fellow, Bader Lab Donnelly CCBR, University of Toronto, Canada http://baderlab.org phone: +1 (416) 978-0571 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with parallel run
This email (as well as the two others) have found their way to the list. No need to post several times! On Wed, Mar 3, 2010 at 12:47, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi all My apologies for the lack of detail in my previous e-mail. I am trying to run gromacs-4.0.7 for a system that I am studying. I have ran several simulations on serial on my own computer that have to date worked fine. I am now however trying to run the simulations on our local cluster in parallel using mpich-1.2.7 and experiencing some difficulty. Please note [...] If you would have searched the mailing list for posts with terms like parallel problem, you probably would have found several posts that report people having serious problems with mpich-1.2.x and the advise to use mpich2, openMPI or LAM/MPI instead. Check with the admins of your Cluster which alternative MPI lib is available or have them install one of the suggested. Oliver -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -merge non interactive
Hallo André, Check the wiki: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive Oliver On Fri, Dec 18, 2009 at 10:59, Wojtyczka, André a.wojtyc...@fz-juelich.de wrote: Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PBC screw
Hi, please someone correct me if I'm wrong, but the equivalent of Gromacs 3.3.x : pbc = full is pbc = xyz periodic_molecules = yes since Gromacs 4.0. Oliver http://manual.gromacs.org/current/online/mdp_opt.html#nl On Thu, Dec 3, 2009 at 08:22, Eudes Fileti fil...@ufabc.edu.br wrote: Hello, grompp 4.0.5 gave me the following error message. ERROR: invalid enum 'full' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'xy' 'screw' Could someone tell me what does the screw option? I cant find it into paper and online manual, as well as at the gmx-list. bests eef -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories
On 6/1/09 11:48 PM, Mark Abraham wrote:
Jinyao Wang wrote:
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
but I am getting the following the fatal error:
Fatal error:
Library file aminoacids.dat not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?
See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
Mark
The procedure on that Wiki-Page actually works in (from my personal experience)
only ~90% of the cases:
After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
actually not set by GMXRC.
Fortunately adding the line:
export GMXLIB=${GMXDATA}/gromacs/top
just after sourcing GMXRC in my .bashrc, worked for me.
Oliver
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
