[gmx-users] Liquid/Liquid
Hi all I want to simulate a biphasic system that I want to arrange the third types of molecules on the interface. would you please introduce to me a good tutorial? I can find a tutorial before but I lost it. Thanks alot Regards Maria -- 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] RMS force is very large for shell MD
Dear gmx users: I have read a paperAtomistic simulation of ion solvation in water explains surface preference of halides, I think it is a perfect work. And I am also interested in the electrolyte behavior at interface. I am using SWM4-NDP polarizable water model and ion Polarizable Alkali and Halide Ions in conjuction with SWM4-NDP water model by GMX4.5.4, I find the RMS force is very large, and at last the system blow up. BUT I simulate pure water with SWM4-NDP water model , It seems everything is OK.I need your help, thanks in advance. Best wishes! Zhongjin He The error: step 177: EM did not converge in 20 iterations, RMS force 0.032 step 178: EM did not converge in 20 iterations, RMS force 0.033 step 179: EM did not converge in 20 iterations, RMS force 0.033 step 180: EM did not converge in 20 iterations, RMS force 0.033 step 181: EM did not converge in 20 iterations, RMS force 0.032 step 182: EM did not converge in 20 iterations, RMS force 0.033 step 183: EM did not converge in 20 iterations, RMS force 0.033 step 184: EM did not converge in 20 iterations, RMS force 0.033 step 185: EM did not converge in 20 iterations, RMS force 0.032 step 186: EM did not converge in 20 iterations, RMS force 0.033 step 187: EM did not converge in 20 iterations, RMS force 0.032 step 188: EM did not converge in 20 iterations, RMS force 0.033 step 189: EM did not converge in 20 iterations, RMS force 0.033 step 190: EM did not converge in 20 iterations, RMS force 0.032 step 191: EM did not converge in 20 iterations, RMS force 0.033 step 192: EM did not converge in 20 iterations, RMS force 0.033 step 193: EM did not converge in 20 iterations, RMS force 0.033 step 194: EM did not converge in 20 iterations, RMS force 0.035 step 195: EM did not converge in 20 iterations, RMS force 0.042 step 196: EM did not converge in 20 iterations, RMS force 1.898 step 197: EM did not converge in 20 iterations, RMS force 49.403 step 198: EM did not converge in 20 iterations, RMS force 173.436 step 199: EM did not converge in 20 iterations, RMS force 363.106 step 200: EM did not converge in 20 iterations, RMS force 589.073 step 201: EM did not converge in 20 iterations, RMS force 786.105 step 202: EM did not converge in 20 iterations, RMS force 845.617 step 203: EM did not converge in 20 iterations, RMS force 773.659 step 204: EM did not converge in 20 iterations, RMS force 741.854 step 205: EM did not converge in 20 iterations, RMS force 778.916 step 206: EM did not converge in 20 iterations, RMS force 964.226 step 207: EM did not converge in 20 iterations, RMS force 1340.912 step 208: EM did not converge in 20 iterations, RMS force 1790.702 step 209: EM did not converge in 20 iterations, RMS force 488.729 step 210: EM did not converge in 20 iterations, RMS force 820.419 step 211: EM did not converge in 20 iterations, RMS force 977.581 step 212: EM did not converge in 20 iterations, RMS force 923.088 step 213: EM did not converge in 20 iterations, RMS force 729.115 step 214: EM did not converge in 20 iterations, RMS force 791.220 step 215: EM did not converge in 20 iterations, RMS force 619.807 step 216: EM did not converge in 20 iterations, RMS force 693.143 step 217: EM did not converge in 20 iterations, RMS force 730.895 step 218: EM did not converge in 20 iterations, RMS force 588.245 step 219: EM did not converge in 20 iterations, RMS force 1110.880 step 220: EM did not converge in 20 iterations, RMS force 1146.601 step 221: EM did not converge in 20 iterations, RMS force 509.965 step 222: EM did not converge in 20 iterations, RMS force 198.761 step 223: EM did not converge in 20 iterations, RMS force 78.372 step 224: EM did not converge in 20 iterations, RMS force 472.341 step 225: EM did not converge in 20 iterations, RMS force 873.614 step 226: EM did not converge in 20 iterations, RMS force 1676.297 step 227: EM did not converge in 20 iterations, RMS force 1731.009 step 227: Water molecule starting at atom 2641 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 228: EM did not converge in 20 iterations, RMS force 0.040 step 228: Water molecule starting at atom 2641 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 229: EM did not converge in 20 iterations, RMS force 0.038 step 230: EM did not converge in 20 iterations, RMS force 0.032 step 230: Water molecule starting at atom 2641 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 231: EM did not converge in 20 iterations, RMS force 0.033 step 232: EM did not converge in 20 iterations, RMS force 0.032 step 232: Water molecule starting at atom 2641 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with
[gmx-users] regarding genbox
Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. -- 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] Liquid/Liquid
Maria Hamilton wrote: Hi all I want to simulate a biphasic system that I want to arrange the third types of molecules on the interface. would you please introduce to me a good tutorial? I can find a tutorial before but I lost it. Google is good at finding things :) Searching Gromacs biphasic system tutorial turns up exactly what you're after. For future reference, all known Gromacs tutorials are linked from: http://www.gromacs.org/Documentation/Tutorials -Justin -- 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] regarding genbox
Ravi Kumar Venkatraman wrote: Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. Assign positions to both solutes within the same box with editconf -box -center (to manually set the COM position rather than allowing -c to put them both in the same place), then concatenate the coordinate files and solvate. -Justin -- 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] regarding genbox
On 15/08/2011 9:22 PM, Justin A. Lemkul wrote: Ravi Kumar Venkatraman wrote: Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. Assign positions to both solutes within the same box with editconf -box -center (to manually set the COM position rather than allowing -c to put them both in the same place), then concatenate the coordinate files and solvate. Alternatively, you can take two coordinate files, one with each solute, and use editconf to translate/rotate them so that their relative position is what you want, then concatenate them with a text editor (making sure not to break the file format), then solvate. Mark -- 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] negative dihedral cp (during cgenff conversion)
On 15/08/2011 10:50 AM, Peter C. Lai wrote: Random noob question: Should the cp field (field 7) in [ dihedraltypes ] always be positive or can it be negative? In the CGenFF conversion, the CHARMM dihedral has: OG302 CG2O2 CG321 CG331 -0.1500 1 180.00 ! LIPID methyl proprionate when I convert to gromacs: [ dihedraltypes ] ; i j k l funcphi0cp mult OG302 CG2O2 CG321 CG331 9 180.0 -0.627601 ;LIPID methyl prop This is the only instance I have seen of a negative number for the dihedral term, so I wonder what the right way to handle it is... (I suppose I could just run it and see...) There are a small minority of CHARMM27 dihedrals that do this. There's no intrinsic reason why the potential should be positive or negative. Forces and energy differences are unaffected by the sign of any component of the energy. Probably they result from optimization of these parameters to reproduce reference quantites in the context of other fixed parameters. Mark -- 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 subject)
Hi all A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mpd file, I got no errors but its seems that this might be too simple. Note there is no relevance in the name umbrella here. Cheers Gavin umbrella1.mdp Description: application/mdp -- 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] bond constraints
Hi all Sorry forgot to give a subject in the first e-mail. A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mdp file, I got no errors but its seems that this might be too simple. Note there is no relevance in the name umbrella here. Cheers Gavin -- 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] bond constraints
Gavin Melaugh wrote: Hi all Sorry forgot to give a subject in the first e-mail. A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mdp file, I got no errors but its seems that this might be too simple. Note there is no relevance in the name umbrella here. You didn't attach the file, but I don't suspect it's relevant anyway. The default algorithm is LINCS. Check mdout.mdp to confirm. In the manual, for keywords with enumerated values, the first one listed is the default, so if no explicit selection is made, the default is used. -Justin -- 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] (no subject)
Hello, Using g_velacc I can calculate the velocity autocorrelation function of a group. Can I calculate the speed of a group instead of velocity ? I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- 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 tool
Hi everyone, Any help will be appreciated, does gromacs have any tool to attach an alkyl chain or RGD to peptide -- 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] Gromacs tool
Dina Kreter wrote: Hi everyone, Any help will be appreciated, does gromacs have any tool to attach an alkyl chain or RGD to peptide Gromacs does not have any molecule-building capacity. There are, of course, many other programs that do: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin -- 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] secondary structure propensities of residues
I am using the latest vesion of DSSP (the one available at DSSP homepage) 2011/8/11 Mark Abraham mark.abra...@anu.edu.au On 10/08/2011 6:03 AM, César Ávila wrote: Hi, I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation fault. Are you using a version of DSSP that is compatible with GROMACS, pre previous discussion of DSSP changes? Mark With gdb I am getting the following messages gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10 GNU gdb (GDB) 7.2-ubuntu Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type show copying and show warranty for details. This GDB was configured as x86_64-linux-gnu. Para las instrucciones de informe de errores, vea: http://www.gnu.org/software/gdb/bugs/... Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se encontraron símbolos de depuración)hecho. (gdb) run Starting program: /usr/local/gromacs/bin/do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10 [Depuración de hilo usando libthread_db enabled] :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.5.4-dev-20110803-e49fb5a (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /usr/local/gromacs/bin/do_dssp (-: Option Filename Type Description -f ../0_trajout.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s ../input/replica_0.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ssdumpdata.dat Output, Opt! Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 17 First frame (ps) to read from trajectory -e time 18 Last frame (ps) to read from trajectory -dt time 10 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -sss string HEBTSecondary structures for structure count Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision) Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision) Program received signal SIGSEGV, Segmentation fault. 0x76ae043c in gmx_strcasecmp () from /usr/local/gromacs/lib/libgmx.so.6 (gdb) bt #0 0x76ae043c in gmx_strcasecmp () from /usr/local/gromacs/lib/libgmx.so.6 #1 0x76ade68f in search_str () from /usr/local/gromacs/lib/libgmx.so.6 #2 0x77b508d4 in bPhobics () from /usr/local/gromacs/lib/libgmxana.so.6 #3 0x0040309a in main () 2011/3/9 Mark Abraham mark.abra...@anu.edu.au On 10/03/2011 1:36 AM, Justin A. Lemkul wrote: ZHAO Lina wrote: Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? The scout.xvg file contains everything you need (in a
[gmx-users] berendsen P coupling and fluctuation properties
Dear all, I noticed that applying Parrinello-Rahman (PR) pressure coupling even after equilibration with berendsen does not lead to target value for pressure when ;Bonds constraints = none is used. I tried Berendsen for to get fixed pressure ( 50 bar) but in the next run PR even for long time is giving 52 bar. This is the case for other target pressures too. So this made me select Berenden which is giving target pressure values but my concern is whether my results are reliable because BR does not give the exact ensemble as PR. I read somewhere on the list that fluctuation properties can not be calculated when BR is used. What does fluctuation property mean? Does this mean that any property calculated form fluctuations of some other quantity can not be obtained? like heat capacity which is defined based on enthalpy fluctuations? I am interested in potential energy terms (g_energy bonded/non boned terms) and structural properties like rdf for a number of polymer molecules, system size around 3000 atoms. Thank you for your comments. Best, constraints = none ;Run control integrator = md dt = 0.002 nsteps = 500 nstcomm = 100 nstenergy = 100 nstxout = 100 nstlist = 10 ns_type = grid coulombtype = Shift vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.25 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 3.5e-5 ref_p = 10 gen_vel = no gen_temp= 300.0 gen_seed= 173529 -- 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] Velocity autocorrelation function
Hello, Using g_velacc I can calculate the velocity autocorrelation function of a group as a vector. Can I calculate the velocity autocorrelation function as a scalar? I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] Hamiltonian replica exchange ?
Hi, I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? 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
Re: [gmx-users] berendsen P coupling and fluctuation properties
On 16/08/2011 7:05 AM, Elisabeth wrote: Dear all, I noticed that applying Parrinello-Rahman (PR) pressure coupling even after equilibration with berendsen does not lead to target value for pressure when ;Bonds constraints = none is used. The use of constraints and the integration step size is linked. Roughly speaking, no constraints should accompany a 0.5 fs time step, H-bond constraints with 1fs and all constraints with 2fs. Haphazard changes to .mdp files have all kinds of these gotchas. I tried Berendsen for to get fixed pressure ( 50 bar) but in the next run PR even for long time is giving 52 bar. This is the case for other target pressures too. You need to be sure to collect statistics only after equilibration, and consider whether the observed variation is consistent with convergence to a given value. So this made me select Berenden which is giving target pressure values but my concern is whether my results are reliable because BR does not give the exact ensemble as PR. I read somewhere on the list that fluctuation properties can not be calculated when BR is used. What does fluctuation property mean? BR does not produce the correct ensemble. I forget the details about why, but there are references in the T-coupling section of the manual you should consider. Does this mean that any property calculated form fluctuations of some other quantity can not be obtained? like heat capacity which is defined based on enthalpy fluctuations? IIRC, yes. I am interested in potential energy terms (g_energy bonded/non boned terms) I routinely struggle to see why people think they can learn anything from these. and structural properties like rdf for a number of polymer molecules, system size around 3000 atoms. Thank you for your comments. Best, constraints = none ;Run control integrator = md dt = 0.002 nsteps = 500 nstcomm = 100 nstenergy = 100 nstxout = 100 nstlist = 10 ns_type = grid coulombtype = Shift vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.25 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = v-rescale tc-grps = System tau_t = 0.1 ref_t = 300 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 3.5e-5 ref_p = 10 gen_vel = no gen_temp= 300.0 gen_seed= 173529 -- 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] secondary structure propensities of residues
On 16/08/2011 7:04 AM, César Ávila wrote: I am using the latest vesion of DSSP (the one available at DSSP homepage) So, as discussed in some thread to which I was referring, there have been some changes to DSSP that prior versions of GROMACS don't cope with. Until GROMACS updates, use a version of DSSP that's at least a year old. Mark 2011/8/11 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 10/08/2011 6:03 AM, César Ávila wrote: Hi, I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation fault. Are you using a version of DSSP that is compatible with GROMACS, pre previous discussion of DSSP changes? Mark With gdb I am getting the following messages gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10 GNU gdb (GDB) 7.2-ubuntu Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type show copying and show warranty for details. This GDB was configured as x86_64-linux-gnu. Para las instrucciones de informe de errores, vea: http://www.gnu.org/software/gdb/bugs/... Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se encontraron símbolos de depuración)hecho. (gdb) run Starting program: /usr/local/gromacs/bin/do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10 [Depuración de hilo usando libthread_db enabled] :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.5.4-dev-20110803-e49fb5a (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /usr/local/gromacs/bin/do_dssp (-: Option Filename Type Description -f ../0_trajout.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s ../input/replica_0.tpr InputStructure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ssdumpdata.dat Output, Opt! Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 17 First frame (ps) to read from trajectory -e time 18 Last frame (ps) to read from trajectory -dt time 10 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -sss string HEBTSecondary structures for structure count Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision) Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision) Program received signal SIGSEGV, Segmentation fault. 0x76ae043c in gmx_strcasecmp () from /usr/local/gromacs/lib/libgmx.so.6
