[gmx-users] Re: RNA simulation (Justin Lemkul)
Thank Justin for your help What forcefield is most suitable to study this case? On Oct 31, 2013 1:56 PM, Hossein Lanjanian hossein.lanjan...@gmail.com wrote: Hi I'm going to study the molecular dynamics of an RNA(which has stem-loop structure) by comparison the native RNA structure and it's mutant to find the conformation changes of 3D structure. This RNA comprises 70 nucleotides. Do you think that it would be possible in Gromacs. -- 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] ligand problem
Hi gmx-users I'm going to study the molecular dynamics of DNA-ligand interaction. I prepared the DNA topology by using the parmbsc0 force field and the ligand by the GAFF force field. My question is: what level of theory (HF/6-31G* or B3lyp/6-31G*) is needed for RESP calculation? can someone help me to address this problem? Best Regards kiana -- 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] ligand problem
Hi, Parmbsc0 is extension of parm99 force-field for which HF/6-31G* was used for charge calculations. Therefore, HF/6-31G* should be used for the RESP calculations. With best regards, Rajendra -- 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] trjconv for pbc
Hi all, I am trying to use trjconv to remove PBC. More specifically, I would like to extract the coordinates of all the water molecules within a certain distance of a single solute molecule. However, I have been unsuccessful in doing so, even after following the guidelines on the GROMACS website (http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions). Here are some of the things I have tried. First, I extracted the indices of the water molecules of interest using g_select and used trjconv to extract the coordinates from the .gro file. Then I used trjconv -pbc mol on the resulting .gro file. The problem is that some of the water molecules are on opposite sides of the box. Does anyone have any suggestions? Thank you very much, Blake PhD Candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] trjconv for pbc
Hi Blake, Centering on the solute should help. Cheers, Tsjerk On Sat, Nov 2, 2013 at 3:55 PM, rankinb rank...@purdue.edu wrote: Hi all, I am trying to use trjconv to remove PBC. More specifically, I would like to extract the coordinates of all the water molecules within a certain distance of a single solute molecule. However, I have been unsuccessful in doing so, even after following the guidelines on the GROMACS website ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions ). Here are some of the things I have tried. First, I extracted the indices of the water molecules of interest using g_select and used trjconv to extract the coordinates from the .gro file. Then I used trjconv -pbc mol on the resulting .gro file. The problem is that some of the water molecules are on opposite sides of the box. Does anyone have any suggestions? Thank you very much, Blake PhD Candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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. -- 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: trjconv for pbc
Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains the water molecules and group 13 is the solute molecule) trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875 trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center Does this procedure seem reasonable? Thanks, Blake -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012162.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_lie and ligand only simulation
On 11/2/13 1:00 AM, Kavyashree M wrote: Dear Gromacs users, I have a protein-ligand in water simulation (Gmx 4.5.3), for calculating free energy of ligand binding, a separate simulation of ligand in water simulation is required (which I read from the list). The question is the protein-ligand is simulated as a dimeric system so is it necessary to simulate the ligand in water as a dimer too. Only if the ligands interact as a dimer in the bound state. If the bind in distinct binding sites within the protein monomers, then no, that wouldn't make much sense to do. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: RNA simulation (Justin Lemkul)
On 11/2/13 6:32 AM, Hossein Lanjanian wrote: Thank Justin for your help What forcefield is most suitable to study this case? The one that your careful study of the literature tells you is the most reliable. It's up to you to justify your choice, not what someone on the Internet tells you :) -Justin On Oct 31, 2013 1:56 PM, Hossein Lanjanian hossein.lanjan...@gmail.com wrote: Hi I'm going to study the molecular dynamics of an RNA(which has stem-loop structure) by comparison the native RNA structure and it's mutant to find the conformation changes of 3D structure. This RNA comprises 70 nucleotides. Do you think that it would be possible in Gromacs. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] g_lie and ligand only simulation
On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: trjconv for pbc
On 11/2/13 11:23 AM, rankinb wrote: Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains the water molecules and group 13 is the solute molecule) trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875 trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center Does this procedure seem reasonable? Right commands, wrong order. 1. Center on the solute 2. Make selection 3. Extract coordinates Note that specifying -b and -e with the same time can fail in some cases; use -dump instead. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: trjconv for pbc
Here is a snapshot of what I was able to extract, if that helps. http://gromacs.5086.x6.nabble.com/file/n5012166/hs.png Blake PhD candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012166.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_lie and ligand only simulation
Sir, Thank you. Should the ligand-water MD be done without PME? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] g_lie and ligand only simulation
On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] g_lie and ligand only simulation
Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
[gmx-users] Re: trjconv for pbc
Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, the resulting coordination shell configuration is not complete in the sense that it looks like the figure I posted previously. In all steps, I used the same .tpr file...is it possible that I need to generate a new one after step 1? Thanks, Blake PhD candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012172.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: trjconv for pbc
On 11/2/13 12:25 PM, rankinb wrote: Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, the resulting coordination shell configuration is not complete in the sense that it looks like the figure I posted previously. In all steps, I used the same .tpr file...is it possible that I need to generate a new one after step 1? 1. trjconv -center -pbc mol -dump 37.875 As long as you're choosing an appropriate index group here (i.e., the single solute molecule of interest), you should not need any further invocations of trjconv before extracting coordinates. Pop open the resulting coordinate file in your favorite visualization software and verify. It should be very obvious if it worked as expected. 2. Make selection 3. Extract -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Gromacs 4.6 4.5.3 qualitative differences 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations
Dear Gromacs Users, I am trying to simulate a system consisting of a vacuum/condensed phase interface in which a 6x6x12nm condensed phase region is flanked on both ends (in the z-dimension) by a 6x6x12nm vacuum region to form overall box dimensions of 6x6x36 nm. The system is a binary liquid mixture of methanol (0.125 mole fraction methanol) in water using a polarizable (charge on a spring) force field (COS/M methanol and COS/G2 water) at 300K and 1bar. The system is stable in Gromacs 4.5.3; however, mdrun gives a segmentation fault in Gromacs 4.6 when attempting to do dynamics (energy minimization completes with no apparent problems). If I remove the vacuum region, mdrun works. If I incrementally add 2 Angstroms to the z-dimension until I reached a vacuum region of 34 Angstroms total (17 Angstroms on both sides of the condensed phase region) and try to simulate these systems, mdrun works every time. When I reach 36 Angstroms, the segmentation fault re-appears. Although not the system I am actually interested in, I did some simulations using Gromacs 4.6 with the 34 Angstrom vacuum region system and observed an undulating and very turbulant vacuum/condensed phase interface in which a column of water/methanol mixture came out of the condensed phase region to connect the two interfaces. Also, the center of mass motion of the system appeared to not have been removed. In contrast, using Gromacs 4.5.3, the interface is not undulating, but is calm and qualitatively planar, no column forms to connect the interfaces, and there is no problem with the center of mass motion removal. Some of the molecules do enter the vacuum region when running with 4.5.3, but this appears to be due to the movement of individual molecules, not a collective motion of many molecules. This system runs fine with a non-polarizable force field in Gromacs 4.6. I have also compared several properties (using g_energy) of the bulk system (no vacuum region) using Gromacs 4.6 and 4.5.3 and they are not the same for the polarizable force field, but they are the same for the non-polarizable force field. Specifically, with the polarizable force field, the LJ(SR) energy is more positive with 4.6, the LJ(LR) energy is more negative with 4.6, the Coulomb(SR) energy is more negative with 4.6, the Could. recip. energy is more negative with 4.6, the polarization energy is more positive with 4.6, the potential energy is more negative in 4.6, the average kinetic energy (and temperature) is the same but the fluctuations are greater in 4.6, the total energy is more negative in 4.6, the pressure looks fine, and the volume looks fine. Where I've noted differences, these are all statistically significant differences. I would like to know if I can just use 4.5.3 and assume the differences between the results of 4.5.3 and 4.6 are due to some problem in 4.6. I am using all the same input files and commands with both versions, only different executables. I ran the regression tests for 4.6 when I installed it, and passed them all. Sincerely, Elizabeth - ADDITIONAL DETAILS: Below is where the problem appears for the interface system when z-dimension of the vacuum region is = 36 Angstroms total. eq4 is my first attempt at dynamics, after three successful energy minimizations (1st: charges screened and no bond constraints, 2nd: charges felt but no bond constraints, 3rd: charges felt and bond constraints on) [ploetz@cluster AddRemainingVacuumBack]$ grompp -f eq4.mdp -c em3.pdb -o eq4.tpr -n index.ndx -p sys.top -nice 0 :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) VERSION 4.6 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -feq4.mdp Inputgrompp input file with MD parameters -po
Re: [gmx-users] Gromacs 4.6 4.5.3 qualitative differences 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations
On 2013-11-02 18:38, ploetz wrote: Dear Gromacs Users, Please start a redmine.gromacs.org issue and assign it to me, but try to simplify the system as much as possible. You can cut and paste all the information to the redmine issue. I am trying to simulate a system consisting of a vacuum/condensed phase interface in which a 6x6x12nm condensed phase region is flanked on both ends (in the z-dimension) by a 6x6x12nm vacuum region to form overall box dimensions of 6x6x36 nm. The system is a binary liquid mixture of methanol (0.125 mole fraction methanol) in water using a polarizable (charge on a spring) force field (COS/M methanol and COS/G2 water) at 300K and 1bar. The system is stable in Gromacs 4.5.3; however, mdrun gives a segmentation fault in Gromacs 4.6 when attempting to do dynamics (energy minimization completes with no apparent problems). If I remove the vacuum region, mdrun works. If I incrementally add 2 Angstroms to the z-dimension until I reached a vacuum region of 34 Angstroms total (17 Angstroms on both sides of the condensed phase region) and try to simulate these systems, mdrun works every time. When I reach 36 Angstroms, the segmentation fault re-appears. Although not the system I am actually interested in, I did some simulations using Gromacs 4.6 with the 34 Angstrom vacuum region system and observed an undulating and very turbulant vacuum/condensed phase interface in which a column of water/methanol mixture came out of the condensed phase region to connect the two interfaces. Also, the center of mass motion of the system appeared to not have been removed. In contrast, using Gromacs 4.5.3, the interface is not undulating, but is calm and qualitatively planar, no column forms to connect the interfaces, and there is no problem with the center of mass motion removal. Some of the molecules do enter the vacuum region when running with 4.5.3, but this appears to be due to the movement of individual molecules, not a collective motion of many molecules. This system runs fine with a non-polarizable force field in Gromacs 4.6. I have also compared several properties (using g_energy) of the bulk system (no vacuum region) using Gromacs 4.6 and 4.5.3 and they are not the same for the polarizable force field, but they are the same for the non-polarizable force field. Specifically, with the polarizable force field, the LJ(SR) energy is more positive with 4.6, the LJ(LR) energy is more negative with 4.6, the Coulomb(SR) energy is more negative with 4.6, the Could. recip. energy is more negative with 4.6, the polarization energy is more positive with 4.6, the potential energy is more negative in 4.6, the average kinetic energy (and temperature) is the same but the fluctuations are greater in 4.6, the total energy is more negative in 4.6, the pressure looks fine, and the volume looks fine. Where I've noted differences, these are all statistically significant differences. I would like to know if I can just use 4.5.3 and assume the differences between the results of 4.5.3 and 4.6 are due to some problem in 4.6. I am using all the same input files and commands with both versions, only different executables. I ran the regression tests for 4.6 when I installed it, and passed them all. Sincerely, Elizabeth - ADDITIONAL DETAILS: Below is where the problem appears for the interface system when z-dimension of the vacuum region is = 36 Angstroms total. eq4 is my first attempt at dynamics, after three successful energy minimizations (1st: charges screened and no bond constraints, 2nd: charges felt but no bond constraints, 3rd: charges felt and bond constraints on) [ploetz@cluster AddRemainingVacuumBack]$ grompp -f eq4.mdp -c em3.pdb -o eq4.tpr -n index.ndx -p sys.top -nice 0 :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) VERSION 4.6 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
[gmx-users] energy minimization problem
Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10. I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful? Best Regards Kiana -- 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] energy minimization problem
On 11/2/13 3:38 PM, kiana moghaddam wrote: Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10. I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful? The purpose of EM is to generate a reasonable configuration that can be subjected to dynamics. For most standard MD, an emtol in the neighborhood of 100-1000 is sufficient, and there are no hard and fast rules that I know of that motivates that choice. If MD fails, run EM again with a lower tolerance. For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and in double precision. As long as the potential energy is negative and in a range that is expected given the size of the system (10^5 - 10^6 in the case of most solvated proteins or membranes), the outcome is probably acceptable. The number of steps is largely irrelevant; the energetic outcome is far more important. I usually set nsteps to some huge value and just let EM converge as far as it will. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] No Distribution?
Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 23 13 And I’m still getting the same error. Any insights? Thanks, Xu Huang -- 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] No Distribution?
On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] No Distribution?
@ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1 23, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] No Distribution?
On 11/2/13 6:50 PM, Xu Dong Huang wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1 23, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. You can't just hope for magic. Please read g_dist -h to understand what the program is doing. Like I said, you have to measure each distance manually, i.e. individually. You need three index groups: [ 1 ] 1 [ 2 ] 2 [ 3 ] 3 Then measure the distances between 12, 23, and 13. Post-process each individually to get the distributions or pool the data (cat the resulting files) and get the distribution from that, if it is in any way meaningful. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Makes sense; the distance between any one group and itself is zero. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] No Distribution?
Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? On Nov 2, 2013, at 6:50 PM, Xu Dong Huang xudonghm...@gmail.com wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 123, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] No Distribution?
On 11/2/13 7:01 PM, Xu Dong Huang wrote: Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? No. If you want three different distances, you need three groups, as I said in my previous message, and I even wrote the exact index file for you. -Justin On Nov 2, 2013, at 6:50 PM, Xu Dong Huang xudonghm...@gmail.com wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1 23, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 23 13 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] No Distribution?
@ Justin, Thanks. I fixed the index files like you suggested. I’m getting logical results now. All the best, On Nov 2, 2013, at 7:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 7:01 PM, Xu Dong Huang wrote: Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? No. If you want three different distances, you need three groups, as I said in my previous message, and I even wrote the exact index file for you. -Justin On Nov 2, 2013, at 6:50 PM, Xu Dong Huang xudonghm...@gmail.com wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 123, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following There are no distances measured, that cannot be right. 0.0000.0000.0000.0000.000 20.0000.0000.0000.0000.000 40.0000.0000.0000.0000.000 60.0000.0000.0000.0000.000 80.0000.0000.0000.0000.000 100.0000.0000.0000.0000.000 120.0000.0000.0000.0000.000 140.0000.0000.0000.0000.000 160.0000.0000.0000.0000.000 180.0000.0000.0000.0000.000 200.0000.0000.0000.0000.000 220.0000.0000.0000.0000.000 240.0000.0000.0000.0000.000 260.0000.0000.0000.0000.000 … Thanks in advance, Xu Huang On Nov 2, 2013, at 6:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 12, 13 and 23, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples : 153 Mean : 0.501255 Standard deviation of the distribution: 0.152864 Standard deviation of the mean: 0.0123583 Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# --- Program g_bond, VERSION 4.5.5 Source code file: gmx_bond.c, line: 207 Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Upon inspecting my index files, I see that it defines my 3 particle group as: [ O1 ] 123 Then I changed the particle group index file to [ O1 ] 12 2 3 1 3 And I’m still getting the same error. Any insights? Use g_dist instead and measure the distances manually. g_analyze can then produce a distribution of those data. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
[gmx-users] DPOSRES and energy minimization
Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = define = -DPOSRES ; IMPLICIT SOLVENT OPTIONS = implicit-solvent = GBSA gb-algorithm = OBC ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 1000 ; ENERGY MINIMIZATION OPTIONS = emtol= 0.1 emstep = 0.01 nstcgsteep = 1000 Thanks! Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.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
