[gmx-users] Fwd: -pbc nojump
I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have another problem. Before using –pbc nojump, there were water molecules in interface of between protein and dna but, After using of –pbc nojump, 1) there was no water molecule in interface of between protein and dna. 2) The distance between water molecules and protein or dna was increased. I want to survey interfacial water molecules and dynamics of water medited hydrogen bonds. I had sent my question to gromacs mailing list, before, but my problem was not solved. -- 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] Fwd: -pbc nojump
On 2010-10-27 09.40, David van der Spoel wrote: I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have another problem. Before using –pbc nojump, there were water molecules in interface of between protein and dna but, After using of –pbc nojump, 1) there was no water molecule in interface of between protein and dna. 2) The distance between water molecules and protein or dna was increased. I want to survey interfacial water molecules and dynamics of water medited hydrogen bonds. try using some of the suggestions that have been posted. e.g. trjorder springs to mind. also if you make claims like The distance between water molecules and protein or dna was increased. you should provide evidence. Either the statement does not say what you mean or you have not measured correctly (e.g. g_mindist). I had sent my question to gromacs mailing list, before, but my problem was not solved. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Fwd: -pbc nojump
Hi, with the nojump option, your water molecules will slowly diffuse out of the home box and appear far away from your protein if you display the MD system with VMD or pymol. You can split your trajectory in two parts (using index groups) and use different options on them individually: a) on the water part (and also on the ions, if they are present), use trjconv -pbc mol b) on the rest, use trjconv -pbc nojump Then overlay both results in the visualization program. Carsten On Oct 27, 2010, at 9:40 AM, David van der Spoel wrote: I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have another problem. Before using –pbc nojump, there were water molecules in interface of between protein and dna but, After using of –pbc nojump, 1) there was no water molecule in interface of between protein and dna. 2) The distance between water molecules and protein or dna was increased. I want to survey interfacial water molecules and dynamics of water medited hydrogen bonds. I had sent my question to gromacs mailing list, before, but my problem was not solved. -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Fwd: -pbc nojump
Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? You said, (Then overlay both results in the visualization program). How? -- 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] Fwd: -pbc nojump
On Oct 27, 2010, at 10:05 AM, leila karami wrote: Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? Yes, I would try it that way. You said, (Then overlay both results in the visualization program). How? In pymol for example, just load both PDBs. Carsten -- 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] Fwd: -pbc nojump
Hi Leila, Maybe you're better off trying: 1. trjconv -pbc nojump # choose system for output 2. trjconv -center -pbc mol # choose protein/dna for centering, system for output Centering is done before removing PBC, so you should be safe with two passes. You might also want to play with -ur to get the best looking representation. Just try some things and see what it does :) Hope it helps, Tsjerk On Wed, Oct 27, 2010 at 10:05 AM, leila karami karami.lei...@gmail.com wrote: Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? You said, (Then overlay both results in the visualization program). How? -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Fwd: -pbc nojump
Dear Tsjerk I did what you said: 1. trjconv -f a.xtc -s a.tpr -o 1.xtc -pbc nojump (system for output) 2. trjconv -f a.xtc -s a.tpr -o 2.xtc -pbc mol –center (pr/dna for centering, system for output) Now, I need new trajectory file for analysis. How I obtain new trajectory file from these two trajectories (1.xtc and 2.xtc) during simulation time? thanks for your help. -- 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] Fwd: -pbc nojump
Dear Carsten and David and Tsjerk Thanks for your time and attention My purpose of these questions is to find a way that 1) close two separated strand of dna (in my case only –pbc nojump fix it) and also 2) water molecules to be put in interface of between protein and dna. Because I want to survey interfacial water molecules and dynamics of water mediated hydrogen bonds. -- 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] the first 10 missing interactions, except for exclusions...
add dihedral parameter for you EPON molecule. Check this: http://oldwww.gromacs.org/pipermail/gmx-users/2005-May/015044.html 2010/10/24 英雄不再寂寞 xiaowu...@qq.com Dear gmxers, I try to simulate a complex system using gmx-4.5.1. I have carried out the minimization without any errors, but when it comes to molecular dynamics, some errors are printed and given below. How to deal with this problem? Please give me some hints. Thanks a lot for any reply. Yours sincerely, Chaofu Wu, Dr. xiaowu...@linux-s38y:~/workshop mdrun -s detamix_md01.tpr -o detamix_md01.trr -c detamix_md01.gro -e detamix_md01.edr -g detamix_md01.log -v -np 4 -N 4 :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.5.1 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, P盲r Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, 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. :-) mdrun (-: Option Filename Type Description .. Option Type Value Description -- .. Getting Loaded... Reading file detamix_md01.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Loaded with Money NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Making 1D domain decomposition 4 x 1 x 1 starting mdrun '40 deta + 100 epon862 + 1 SWCNT(10,10)' 400 steps, 4000.0 ps. step 0 NOTE: Turning on dynamic load balancing step 39500, will finish Mon Oct 25 02:51:47 2010vol 0.61 imb F 14% A list of missing interactions: Ryckaert-Bell. of 12880 missing 2 Molecule type 'EPON' the first 10 missing interactions, except for exclusions: Ryckaert-Bell. atoms 11 12 14 16 global 5481 5482 5484 5486 Ryckaert-Bell. atoms 16 21 23 11 global 5486 5491 5493 5481 --- Program mdrun, VERSION 4.5.1 Source code file: domdec_top.c, line: 356 Fatal error: 2 of the 79000 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.5 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Jede der Scherben spiegelt das Licht (Wir sind Helden) xiaowu...@linux-s38y:~/workshop -- 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 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] Percentage of H-bonds
Carla Jamous wrote: Hi Justin, I guess the problem is in the way I concatenate my trajectory. So my question may seem stupid but I can't seem to understand this part of the manual: c (continue) - The start time is taken from the end of the previous file. Use it when your continuation run restarts with t=0. l (last) - The time in this file will be changed the same amount as in the previous. Use it when the time in the new run continues from the end of the previous one, since this takes possible overlap into account. Where is this in the manual? When I use trjcat to concatenate three different trajectories: trjcat -f traj1.xtc traj2.xtc traj3.xtc -o traj_cat.xtc -settime Should I use c or l? I see no way to incorporate any such option, if it even exists - what version of Gromacs are you using? In any case, the use of -settime makes all of this irrelevant. You're specifically setting the start time of each of the trajectories. Use gmxcheck to make sure you got what you think you did. What is the reason for -settime? Are the trajectories non-continuous? I'm CC'ing this back to the list. I only offered to take a look at your files off-list. Further questions and feedback need to stay on gmx-users. -Justin Thanks, Carla On Tue, Oct 26, 2010 at 2:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Yes, I'm always looking at the same one, it means the corresponding one in the other trajectory. If you want me to try to figure out what's going on, send me your .xpm and .ndx files (off-list), as well as a description of what I'm looking for and why you think it shouldn't be there. -Justin Carla On Tue, Oct 26, 2010 at 2:17 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Please I have a problem: I concatenated 3 trajectories and got one long trajectory on which I ran the perl script it gives me lets say 60% for hbond 1. But when I look in each of the 3 trajectories alone, this hbond doesn't even exist in 2 of them. Do you have an idea where the problem might be because I checked if it's well concatenated and it is. And I can't figure out why I have this error. The hydrogen bond indices are regenerated in each trajectory, since not all H-bonds might be present in the same order. Are you sure you're continually looking at the same one? -Justin Thanks, Carla On Tue, Oct 26, 2010 at 2:08 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Carla Jamous wrote: Hi Justin, Please can you explain this particular comment in your perl script: # There should now be $nres lines left in the file # The HB map for the last index is written first (top-down in .xpm file) # * Element 0 is index $nres, element 1 is $nres-1, etc. Is the perl script reading the index file beginning from the bottom? If so, why is that? Because in the manual, it says that in the matrix, the ordering is identical to that in the index file. The order is the same, and the indices are mapped exactly as you would expect them. The .xpm file is written, however, from top down. So the final index in hbond.ndx is the top line in the matrix. As such, even though they are in the same order, per se, the two files (.xpm and .ndx) have to be read in opposite directions. -Justin Thank you. Carla On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:
Re: [gmx-users] Fwd: -pbc nojump
Hi Leila, 2.xtc should contain all that you want. My point was that you shouldn't need to separate protein/dna and solvent into two trajectories to be combined later. Note that this only concerns visualization. You can do distance and H-bond calculations on the original trajectory, as the relevant tools know how to deal with PBC. Cheers, Tsjerk On Wed, Oct 27, 2010 at 12:01 PM, leila karami karami.lei...@gmail.com wrote: Dear Carsten and David and Tsjerk Thanks for your time and attention My purpose of these questions is to find a way that 1) close two separated strand of dna (in my case only –pbc nojump fix it) and also 2) water molecules to be put in interface of between protein and dna. Because I want to survey interfacial water molecules and dynamics of water mediated hydrogen bonds. -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Fwd: -pbc nojump
Dear Tsjerk Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns visualization. Thus, can I use old xtc file (with out –pbc nojump) for analysis such as interfacial waters and water mediated hydrogen bonds or every other analysis? -- 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] Electrostatic interactions between residues
Hi everyone, please is there a way to know if electrostatic interactions exist between my ligand and my protein during the trajectory? Which tool can I use for this purpose, other than g_saltbr? Thank you, Carla -- 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] Fwd: -pbc nojump
Right :) On Wed, Oct 27, 2010 at 2:27 PM, leila karami karami.lei...@gmail.com wrote: Dear Tsjerk Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns visualization. Thus, can I use old xtc file (with out –pbc nojump) for analysis such as interfacial waters and water mediated hydrogen bonds or every other analysis? -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] absolute reference for pulling and center of mass removal
Bert, instead of directly answering your question, let me suggest that you don't want to pull in absolute coordinates. Probably, you want to pull your polymer with respect to the position of some other (non-water) reference group. The only reason that I can think of to use absolute coordinates it a) testing or b) you really want to simulate non-equilibrium (but perhaps steady state) flow properties like turbulence. In the latter case, you can probably use constant force pulling and ignore the warning. If you're thinking of something else, please tell us what you want to achieve. Chris. Dear gmx-users? I intend to pull a polymer in the bulk water using the pull code in gmx4. When I checked the manual, it was said With an absolute reference the system is no longer translation invariant and one should think about what to do with the center of mass motion. Yes, I set the pull group with the polymer and the reference group with the default (0,0,0). Then I received a warning after grompp as follows: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. I am not sure about the artifacts artifacts, could somebody give me a more definite explanation. Assuming we pull the COM of the polymer along x, and then the COM of water in x is coupled with that of the polymer, but the COM of water in yz is uncoupled. As a result, the momentum of system in yz could be nonzero for long time simulations if no COM removal is applied in yz. So to speak, if we do not remove the COM motion, artifacets could be induced by round errors in uncoupled yz direction. Am I right? How the deal with the COM removal in this case? I have done two tests here: 1) Set comm-grps = system. The polymer and the water flowed in the negative direction. 2) Set comm-grps = polymer SOL. The polymer still moved in x, and no COM motion observed for SOL. Which one could be appropriate, and if both are not ok, is there a way to solve the problems? Thanks for your suggestions in advance! Best regards, Bert -- 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] Electrostatic interactions between residues
Carla Jamous wrote: Hi everyone, please is there a way to know if electrostatic interactions exist between my ligand and my protein during the trajectory? Which tool can I use for this purpose, other than g_saltbr? You can quantify short-range nonbonded energies using energygrps, which at this point would require using the -rerun feature of mdrun. You can also get a list of contacts using g_mindist and/or g_dist, as well as distance matrices with g_mdmat. -Justin Thank you, Carla -- 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 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] Error in trjconv
Hi, While using trjconv I get this error: VMD_PLUGIN_PATH not set. Using default location: /usr/local/lib/vmd/plugins/*/molfile No VMD Plugins found Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the VMD installation. The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match. --- Program trjconv, VERSION 4.5.1 Source code file: trxio.c, line: 863 Fatal error: Not supported in read_first_frame: nanorest_1_nvt.tpr Can anyone help in thsi regard? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] Error in trjconv
Sai Pooja wrote: Hi, While using trjconv I get this error: VMD_PLUGIN_PATH not set. Using default location: /usr/local/lib/vmd/plugins/*/molfile No VMD Plugins found Set the environment variable VMD_PLUGIN_PATH to the molfile folder within the VMD installation. The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match. --- Program trjconv, VERSION 4.5.1 Source code file: trxio.c, line: 863 Fatal error: Not supported in read_first_frame: nanorest_1_nvt.tpr Can anyone help in thsi regard? Without your command line, it's hard to say exactly what went wrong (HINT: always provide your exact command when a tool fails), but based on the fact that trjconv is trying to read a frame (a trajectory operation) from a .tpr file and invoking the VMD conversion routines, I'd suspect you've passed a .tpr file to -f instead of -s. -Justin Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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 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] About Zn paramter
Dear all I am including the parameter for the Zinc in the topology file all the bonded and nonbonded parameters have been included in the topology still it is not accepting the parameter the Zn atom move away from the coordination. Thanking you in advance E R Azhagiya singam -- 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] About Zn paramter
babu gokul wrote: Dear all I am including the parameter for the Zinc in the topology file all the bonded and nonbonded parameters have been included in the topology still it is not accepting the parameter the Zn atom move away from the coordination. Have you actually specified bonds between the Zn and its coordinating residues? Such a task is not trivial to define, and would likely require thorough reparameterization of all species involved. In any case, if there are actual bonds, they cannot be broken. If you are relying simply on nonbonded interactions to hold Zn in place, this may not work and likely represents a deficiency in the model. If you can justify doing so (i.e., defend against reviewer criticism), then you might be able to apply distance restraints to keep the position of Zn relatively consistent. Always keep in mind: http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin Thanking you in advance E R Azhagiya singam -- 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 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] United atom forcefield for long alkane ?
Hi, I was planning to simulate a system of long-chain alkane carboxylate in water with a chemical formula CH3-(CH2)_20-COOH . For that I was thinking of using an united atom force-field. I found , in gromacs, there are two United atom force-field available: GROMOS-96 and OPLS-UA. I was wondering whether some one can suggest which united atom force-field will be good choice for such a long chain alkane chain ? Thanks Sanku -- 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] viscosity calculations
Hello, I am trying to calculate the viscosity of my pure water system at 275K. The system has run for 40ns. I issued the following command: g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis sixsitewater_275K -b 0 -e 4 The numbers I get in the output file are almost 100 times bigger than reported literature. Am I doing something wrong or in the analysis procedure sth is not divided properly? Also, I tried to calculate the viscosity through the transverse current autocorrelation function. The command I issued was: g_tcaf_d_mpi -f 275K_50_50_50_2.trr -s 275K_50_50_50_2.tpr -oc 275K_50_50_50_2 -ov 275K_50_50_50_2 -mol -wt 5 -n watermolecules.ndx The output is: k 1.253 tau 2.383 eta 0.14641 10^-3 kg/(m s) irow = 2, icol = 2 2225392908111942225202360202531386163200.000 -0.195 0.195 0.000 Numerical Recipes run-time error... GAUSSJ: Singular Matrix-2 Fit failed! k 1.253 tau 1.000 eta 0.15845 10^-3 kg/(m s) k 1.253 tau 0.133 eta 0.44011 10^-3 kg/(m s) k 1.771 tau 0.455 eta 0.10514 10^-3 kg/(m s) k 1.771 tau 1.458 eta 0.08329 10^-3 kg/(m s) k 1.771 tau 0.348 eta 0.13366 10^-3 kg/(m s) k 1.771 tau 0.324 eta 0.27031 10^-3 kg/(m s) k 1.771 tau 0.320 eta 0.14002 10^-3 kg/(m s) k 1.771 tau 2.100 eta 0.07649 10^-3 kg/(m s) k 2.169 tau 1.541 eta 0.05321 10^-3 kg/(m s) k 2.169 tau 2.201 eta 0.04949 10^-3 kg/(m s) irow = 1, icol = 1 0.000 -0.126 0.126 708363867825344.750 Numerical Recipes run-time error... GAUSSJ: Singular Matrix-2 Fit failed! k 2.169 tau 1.000 eta 0.05282 10^-3 kg/(m s) k 2.169 tau 0.997 eta 0.07365 10^-3 kg/(m s) k 2.505 tau 0.511 eta 0.05450 10^-3 kg/(m s) irow = 1, icol = 1 0.000 0.710 -0.710 34533840121856978944.000 Numerical Recipes run-time error... GAUSSJ: Singular Matrix-2 Fit failed! k 2.505 tau 1.000 eta 0.03961 10^-3 kg/(m s) k 2.505 tau 0.248 eta 0.06944 10^-3 kg/(m s) Averaged over k-vectors: k 1.253 tau 0.529 Omega 1.189 eta 0.35612 10^-3 kg/(m s) k 1.771 tau 0.458 Omega 0.832 eta 0.14388 10^-3 kg/(m s) k 2.169 tau 1.540 Omega 1.601 eta 0.05491 10^-3 kg/(m s) k 2.505 tau 0.280 Omega 0.499 eta 0.07050 10^-3 kg/(m s) I do not understand the failure parts of the output, also what should I do with the output numbers? I took a look at the -ov output. The final 4 numbers are not fittable on a eta(k)=eta(0)*(1-ak^2). Am I fitting the wrong data? Sorry for such a huge e-mail. Paymon -- 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] Dihedral energy map along two eigenvectors to actual conformations
Hi all, I have been following the method outlined by Yuguang Mu to generate the energy landscape along two eigenvectors. There are four minima that I wish to explore. I can determine the points along the vectors that correspond to the conformation, but am unsure of how to use those to obtain the corresponding pdb as was shown in the paper: Mu, et al. Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis, 2005. Any insight? Cordially, Ali -- 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] Dihedral energy map along two eigenvectors to actual conformations
Ali Naqvi wrote: Hi all, I have been following the method outlined by Yuguang Mu to generate the energy landscape along two eigenvectors. There are four minima that I wish to explore. I can determine the points along the vectors that correspond to the conformation, but am unsure of how to use those to obtain the corresponding pdb as was shown in the paper: Mu, et al. Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis, 2005. Any insight? Have you tried the dihedral PCA how-to? I don't know if it will give you everything you want, but it's certainly a start. http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA -Justin Cordially, Ali -- 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 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] United atom forcefield for long alkane ?
Check the original specifications for each of those force fields, then check to see if the molecule you are wanting to simulate falls within the boundaries of how the force field was derived. Also search the literature for simulations of the same or similar molecules, and see which force fields they used. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - 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 Sanku M Sent: Thursday, 28 October 2010 6:06 AM To: gmx-users@gromacs.org Subject: [gmx-users] United atom forcefield for long alkane ? Hi, I was planning to simulate a system of long-chain alkane carboxylate in water with a chemical formula CH3-(CH2)_20-COOH . For that I was thinking of using an united atom force-field. I found , in gromacs, there are two United atom force-field available: GROMOS-96 and OPLS-UA. I was wondering whether some one can suggest which united atom force-field will be good choice for such a long chain alkane chain ? Thanks Sanku -- 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] g_rama: Dihedral not found in topology
I am getting the following warning message from g_rama, even for a simple system like a blocked Alanine dipeptide: $ g_rama -s test.tpr -f traj.xtc […] Reading file test.tpr, VERSION 4.5.1 (single precision) Found 1 phi-psi combinations Dihedral around 6,8 not found in topology. Using mult=3 […] I have attached the files required to reproduce this problem. The two backbone dihedral angles for this systems are for the atom sets (5,7,9,15) and (7,9,15,17), and both groups appear in the [ dihedrals ] section of the topology file (and also exist in the tpr file). This happens using Gromacs 4.5.1 and 4.0.7. If you would like to reproduce this behavior, I have attached a small test set (never mind that the simulation doesn't necessarily make sense). I used the following sequence of commands: grompp -f test.mdp -c initial.gro -p topol.top -o test.tpr mdrun -s test.tpr g_rama -s test.tpr -f traj.xtc While the output of g_rama looks reasonable, the warning message makes me worried that I might have missed something in the topology file. Thanks, Lutz test.mdp Description: Binary data initial.gro Description: Binary data topol.top Description: Binary data -- 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] Dihedral energy map along two eigenvectors to actual conformations
Yes I have been using the how-to for making the energy landscape. Now I just need to go backwards. Ali Naqvi wrote: Hi all, I have been following the method outlined by Yuguang Mu to generate the energy landscape along two eigenvectors. There are four minima that I wish to explore. I can determine the points along the vectors that correspond to the conformation, but am unsure of how to use those to obtain the corresponding pdb as was shown in the paper: Mu, et al. Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis, 2005. Any insight? Have you tried the dihedral PCA how-to? I don't know if it will give you everything you want, but it's certainly a start. http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA -Justin Cordially, Ali -- 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-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! End of gmx-users Digest, Vol 78, Issue 212 ** -- 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] Re: Gromacs problem
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list on this message; I would ask that you post anything further there. To solve your problem, please see the following document: http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation Do not use the test set; its current incarnation is useless. This is stated on the website in several locations. -Justin mustafa bilsel wrote: Dear Justin, I am a new Gromacs user. Although I havenot seen any problem while installing, I have a problem with the test of Gromacs. I see the following error message. ERROR: Can not find grompp in your path. Please source GMXRC and try again. What should I understand from this message? I have Gromacs 4.5 and gmxtest-4.0.4 set. Best wishes Mustafa Bilsel -- 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 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] problem of paralleled running
Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! All the best, fancy -- 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] problem of paralleled running
On October 28, 2010 at 4:05 AM fancy2012 fancy2...@yeah.net wrote: Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, butwhen I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! Gromacs 4.5.1 is somewhat viral on cpu (takes all of them if not told otherwise). I you submit multiple jobs to a node without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure. All the best, fancy TJ Mustard Email: musta...@onid.orst.edu -- 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] problem of paralleled running
On October 28, 2010 at 4:11 AM TJ Mustard musta...@onid.orst.edu wrote: On October 28, 2010 at 4:05 AM fancy2012 fancy2...@yeah.net wrote: Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, butwhen I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! Gromacs 4.5.1 is somewhat viral on cpu (takes all of them if not told otherwise). I you submit multiple jobs to a node without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure. If you use SGE, you may want to use SMP or MPI. All the best, fancy TJ Mustard Email: musta...@onid.orst.edu TJ Mustard Email: musta...@onid.orst.edu -- 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] problem of paralleled running
Can't help you directly, other than suggestion you provide a lot more information than you have. Direct copy/paste of the command lines used, error messages and log files generated, how GROMACS was installed etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - 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 fancy2012 Sent: Thursday, 28 October 2010 1:05 PM To: gmx-users Subject: [gmx-users] problem of paralleled running Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! All the best, fancy -- 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] problem of paralleled running
fancy2012 wrote: Dear GMX users, I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much! To get a faster resolution, you should provide substantially more detail, including: 1. Commands given to install Gromacs 2. Description of hardware, compilers, etc. 3. Command issued that causes the problem 4. The actual error message (from Gromacs, OS, MPI, etc.), if any -Justin All the best, fancy -- 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 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] Problems for checking the equilibrium of Ionic liquid system
Dear GMX users, Now, I am doing some simulations about ionic liquids. The problem I am encountering is how to check the equilibrium of Ionic liquid system. The boss asks me to do the RSMD to check it, but I think it is not right. Could you give me some useful advice? Thank you very much for your attentions! With best wishes! Hui Sun -- 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
