Re: [gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times
Creighton Buie wrote: Hello Gromacs Community, I am trying to set up a system where there is a coarse grained hydrophobic polymer floor in a solvated water box. I am using the martini force field with an .itp file for the polymer. The floor is basically the polymer spaced 0.5 nm apart from each other and the bottom bead is fixed in the X, Y, and Z direction. I have tried many ways of fixing this bead using both freeze groups and position restrained techniques, both to no avail. I am using PME and no part of the system has a charge. The latest try has consisted of using the position restrain line in the .itp file of the polymer through the topology file and fixing the bottom bead with a force of 1000 in X Y Z. The energy minimization run went smoothly but when I try to do any type of md I get this error message: Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of432 missing 1 --- Program mdrun, VERSION 4.0.3 Source code file: domdec_top.c, line: 172 Software inconsistency error: Some interactions seem to be assigned multiple times --- You Can Always Go On Ricky Lake (Offspring) After searching the mailing list about this error I could only find that it was a bug. Is this correct? Any suggestions is much appreciated. If so, you should try an up-to-date version of GROMACS - 4.0.4 is current. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replacement for G43b1 force field?
From the archives, a simple search for 43b1 4.0: http://www.gromacs.org/pipermail/gmx-users/2008-December/038463.html -Justin Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation of a GPCR protein using GROMACS vacuum force field. I want to use the old force field G43b1 (vacuum simulation) which is not there in GROMACS4.0.3. I would like to know which is the substitute for this G43b1 force field from the present menu: Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Should I use the 8th one? The new manual for GROMACS4.0 also does not reflect this change. Any suggestion is welcome. Regards,// // *Anirban Ghosh* *Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India * Share files, take polls, and make new friends - all under one roof. Click here. http://in.rd.yahoo.com/tagline_groups_8/*http://in.promos.yahoo.com/groups/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Replacement for G43b1 force field?
Hi ALL, I want to do a MD simulation of a GPCR protein using GROMACS vacuum force field. I want to use the old force field G43b1 (vacuum simulation) which is not there in GROMACS4.0.3. I would like to know which is the substitute for this G43b1 force field from the present menu: Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges Should I use the 8th one? The new manual for GROMACS4.0 also does not reflect this change. Any suggestion is welcome. Regards, Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] No targets specified and no makefile found
Hi everybody, Whilst attempting to compile gromacs 4 on my MacOSX I encountered a problem. I successfully configured with ./configure but the 'make' command doesn't work. It displays: MBSTEFANO:gromacs-4.0.4 Stefano$ make make: *** No targets specified and no makefile found. Stop. Any suggestions? Cheers, Stefano. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No targets specified and no makefile found
Stefano Meliga wrote: Hi everybody, Whilst attempting to compile gromacs 4 on my MacOSX I encountered a problem. I successfully configured with ./configure but the 'make' command doesn't work. It displays: MBSTEFANO:gromacs-4.0.4 Stefano$ make make: *** No targets specified and no makefile found. Stop. Then the Makefile was not created, and ./configure did not successfully finish. Check config.log for error messages. -Justin Any suggestions? Cheers, Stefano. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with energy min. in membrane tutorial
Hello, I was following the steps in Justin Lemkul's tutorial for insertion of a protein in a lipid bilayer and have come accross a problem right after using inflategro's script from Tieleman's website. It says there that I should run an energy minimization and then continue with the steps of the tutorial. Well, I have used the output structure from inflategro to run an energy minimisation using grompp/mdrun using a steepest descent algorithm. The problem is that when I type the command: grompp -f em_steep.mdp -c inflatedbilayer.gro -p topol.top -o inflatedbilayer.tpr The following errors appear: ERROR 1 [file topol.top, line 523]: No default G96Angle types ERROR 2 [file topol.top, line 794]: No default Proper Dih. types It seems that I have made some mistake with the forcefield's parameter files, but I have tried to do everything all over again and the same errors occur. Has anyone had any similar problem? I would appreciate some help if possible. Thank you Fabrício Bracht ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with energy min. in membrane tutorial
Ragnarok sdf wrote: Hello, I was following the steps in Justin Lemkul's tutorial for insertion of a protein in a lipid bilayer and have come accross a problem right after using inflategro's script from Tieleman's website. It says there that I should run an energy minimization and then continue with the steps of the tutorial. Well, I have used the output structure from inflategro to run an energy minimisation using grompp/mdrun using a steepest descent algorithm. The problem is that when I type the command: grompp -f em_steep.mdp -c inflatedbilayer.gro -p topol.top -o inflatedbilayer.tpr The following errors appear: ERROR 1 [file topol.top, line 523]: No default G96Angle types ERROR 2 [file topol.top, line 794]: No default Proper Dih. types So what are on these lines? If you can identify which atoms these correspond to, you will be able to determine whether or not parameters for this angle and dihedral actually exist within the force field. -Justin It seems that I have made some mistake with the forcefield's parameter files, but I have tried to do everything all over again and the same errors occur. Has anyone had any similar problem? I would appreciate some help if possible. Thank you Fabrício Bracht ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run pdb2gmx using the following two files. I still got the similar error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading pdms2.pdb... Read 13 atoms Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 13 atoms chain #res #atoms 1 ' ' 3 13 All occupancies are one Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx_d, VERSION 4.0.4 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- My new residue added to ffoplass.rtp is: [ PDM ] ; designation arbitrary, C1 and C2 is -CH3 [ atoms ] SI1 SI 0.3001 C1 opls_069 0.0001 C2 opls_069 0.0001 O1 opls_108-0.3001 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 O1 O1 +SI1 ; Terminal PDMS residue (beginning of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDMB ] [ atoms ] C1opls_069 0.0001 SI1SI 0.3001 C2opls_069 0.0001 C3opls_069 0.0001 O1opls_108-0.3001 [ bonds ] SI1 C1 SI1 C2 SI1 C3 SI1 O1 O1 +SI1 ; Terminal PE residue (end of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDME ] [ atoms ] SI1SI 0.0001 C1opls_069 0.0001 C2opls_069 0.0001 C3opls_069 0.0001 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 C3 PDB file: ATOM 1 SI1 PDMB1 8.995 -3.779 -2.091 1.00 0.00 ATOM 2 C1 PDMB1 10.682 -3.453 -2.828 1.00 0.00 ATOM 3 C2 PDMB1 8.020 -2.184 -2.039 1.00 0.00 ATOM 4 O1 PDMB1 8.142 -4.958 -3.082 1.00 0.00 ATOM 5 C3 PDMB1 9.192 -4.446 -0.356 1.00 0.00 ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00 ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00 ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00 ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00 ATOM 10 SI1 PDME3 6.370 -8.062 -6.022 1.00 0.00 ATOM 11 C1 PDME3 7.679 -8.351 -7.325 1.00 0.00 ATOM 12 C2 PDME3 5.990 -9.673 -5.153 1.00 0.00 ATOM 13 C3 PDME3 4.816 -7.411 -6.834 1.00 0.00 TER Thanks a lot! On Thu, Apr 30, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Your system works for me under Gromacs 4.0.4 - the only issue is that your PDME residue has a net +0.3 charge. Does your Gromacs installation work properly for proven systems like proteins? I would suggest upgrading to version 4.0.4 and trying again. If that does not work, post to the list a complete description of your hardware and software - OS, version, compilers used, configuration options, etc, and see if anyone can spot a problem. -Justin Yanmei Song wrote: Sorry to bother so many times. I edited the rtp and added the new residue as following, which I think should be no problem. [ PDM ] [ atoms ] SI1 SI 0.300 1 C1 opls_069 0.000 1 C2 opls_069 0.000 1 O1 opls_108 -0.300 1 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 O1 O1 +SI1 ; Terminal PDMS residue (beginning of chain) [ PDMB ] [ atoms ] C1 opls_069 0.000 1 SI1 SI 0.300 1 C2 opls_069 0.000 1 C3 opls_069 0.000 1 O1 opls_108 -0.300 1 [ bonds ] SI1 C1 SI1 C2 SI1 C3 SI1
Re: [gmx-users] Error by pdb2gmx
Then it seems clear to me that your installation of Gromacs is faulty. Have you tried running the test set (available on the wiki site)? If you can describe your computer system (OS, version, compilers used, configuration options, etc.) then perhaps someone on the list can spot a potential pitfall. -Justin Yanmei Song wrote: Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run pdb2gmx using the following two files. I still got the similar error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading pdms2.pdb... Read 13 atoms Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 13 atoms chain #res #atoms 1 ' ' 3 13 All occupancies are one Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx_d, VERSION 4.0.4 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- My new residue added to ffoplass.rtp is: [ PDM ] ; designation arbitrary, C1 and C2 is -CH3 [ atoms ] SI1 SI 0.3001 C1 opls_069 0.0001 C2 opls_069 0.0001 O1 opls_108-0.3001 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 O1 O1 +SI1 ; Terminal PDMS residue (beginning of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDMB ] [ atoms ] C1opls_069 0.0001 SI1SI 0.3001 C2opls_069 0.0001 C3opls_069 0.0001 O1opls_108-0.3001 [ bonds ] SI1 C1 SI1 C2 SI1 C3 SI1 O1 O1 +SI1 ; Terminal PE residue (end of chain) ; designation arbitrary, C1 C2 and C3 is -CH3 [ PDME ] [ atoms ] SI1SI 0.0001 C1opls_069 0.0001 C2opls_069 0.0001 C3opls_069 0.0001 [ bonds ] SI1 -O1 SI1 C1 SI1 C2 SI1 C3 PDB file: ATOM 1 SI1 PDMB1 8.995 -3.779 -2.091 1.00 0.00 ATOM 2 C1 PDMB1 10.682 -3.453 -2.828 1.00 0.00 ATOM 3 C2 PDMB1 8.020 -2.184 -2.039 1.00 0.00 ATOM 4 O1 PDMB1 8.142 -4.958 -3.082 1.00 0.00 ATOM 5 C3 PDMB1 9.192 -4.446 -0.356 1.00 0.00 ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00 ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00 ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00 ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00 ATOM 10 SI1 PDME3 6.370 -8.062 -6.022 1.00 0.00 ATOM 11 C1 PDME3 7.679 -8.351 -7.325 1.00 0.00 ATOM 12 C2 PDME3 5.990 -9.673 -5.153 1.00 0.00 ATOM 13 C3 PDME3 4.816 -7.411 -6.834 1.00 0.00 TER Thanks a lot! On Thu, Apr 30, 2009 at 5:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Your system works for me under Gromacs 4.0.4 - the only issue is that your PDME residue has a net +0.3 charge. Does your Gromacs installation work properly for proven systems like proteins? I would suggest upgrading to version 4.0.4 and trying again. If that does not work, post to the list a complete description of your hardware and software - OS, version, compilers used, configuration options, etc, and see if anyone can spot a problem. -Justin Yanmei Song wrote: Sorry to bother so many times. I edited the rtp and added the new residue as following, which I think should be no problem. [ PDM ] [ atoms ] SI1SI 0.3001 C1 opls_069 0.0001 C2 opls_069 0.0001 O1 opls_108-0.3001 [ bonds ] SI1 -O1 SI1C1 SI1C2 SI1O1 O1
[gmx-users] Problems with tabulated potentials
Dear all; I ran a simulation using two tabulated potentials for two energy groups but it seems that Gromacs is not generating any potential because LJ energies = 0. in every step. The groups are TET and HS and they are represented in index.ndx. Their tabulated potentials are table_TET_TET.xvg and table_HS_HS.xvg respectively. The charge of every atom is zero and the Gromacs version is 3.3.3. My parameter and md.log files are: Parameter file ### integrator = sd dt = 0.001 nsteps = 10 nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 1000 nstenergy= 1000 nstxtcout= 100 xtc_grps = System energygrps = TET HS energygrp_table = TET TET HS HS energygrp_excl = TET HS nstlist = 10 ns_type = grid rlist= 1.0 coulombtype = User rcoulomb = 1.0 epsilon_rf = 80 vdwtype = User rvdw = 1.0 tcoupl = Berendsen tc-grps = System tau_t= 0.2 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.46e-5 ref_p= 1.0 gen_vel = yes gen_temp = 300 gen_seed =-1 ### tables: table_TET_TET.xvgtable_HS_HS.xvg mdrun_mpi -s topol.tpr -table table.xvg -x traj -o traj -g md ## md.log file ## . . . Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 0.000 Read user tables from table_TET_TET.xvg with 12582 data points. Tabscale = 4838.85 points/nm Read user tables from table_HS_HS.xvg with 12402 data points. Tabscale = 4769.62 points/nm . . . Step Time Lambda 23000 23.00.0 Energies (kJ/mol) Bond AngleLJ (SR) Coulomb (SR) Potential 4.79413e+032.18701e+030.0e+000.0e+006.98115e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 1.36561e+042.06372e+043.04239e+027.13050e+01 . . . A V E R A G E S == ### == ... Epot (kJ/mol)Coul-SR LJ-SR TET-TET0.0e+000.0e+00 TET-HS0.0e+000.0e+00 HS-HS0.0e+000.0e+00 . . . ## Could you please tell me what is wrong ? P.S. even I have tried: mdrun_mpi -s topol.tpr -table table.xvg -tablep table_TET_TET.xvg table_HS_HS.xvg -x traj -o traj -g md But I got the same result. Thanks in advance, Harry G. _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd1_052009___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] configuration does not change in minim ization trajectory
heiko...@web.de wrote: Hello all, I am doing a cg minimization with Gromacs-4.0.3. It is compiled on a Linux system with gcc 3.4.6 All frames in the trajectory are identical to the starting configuration, except for the final one, which is clearly different. How are you assessing this? External viewing programs don't always show the necessary level of detail. If you use trjconv -dump to drop out a few select frames, and diff the resulting .gro files, are they indeed identical, or are there small differences? All configurations but the last one are strictly identical to the first. (Determined as suggested, using diff on .gro files dumped from the trajectory) I see something similar with my own CG trajectories. I do not routinely inspect them; I typically rely on the energy curve and final output structure to determine the adequacy of the procedure. What I find in my own case is that the third decimal differs by no more than 1 unit between the reference structure and the constituent frames of the .trr file. It would seem to me that if you are seeing no difference along the different frames, this is probably just a machine precision issue. Differences are more obvious, however, when using steepest descents, and the trajectory, when viewed in VMD, shows continual change in the structure. How different is the final structure? Is there a drastic change? Or is it just that the change relative to the input structure is more obvious? The rmsd between the first and last structures is about 0.1 nm, using -nomw with g_rms. So any changes to the structure are local, but obvious in VMD. I would think that 0.1 nm is somewhat large for a simple minimization procedure, although this is probably dependent upon system size and which components you are analyzing. -Justin I get the expected number of frames in the trajectory (.trr), and the energy saved in the .edr is decreasing. But apparently the changes in the structure do not reach the trajectory file. If the energy is changing, then so too should the structure. I agree, internally the structure must be changing, only the output does not show it. -Justin Any suggestions? Heiko Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Thanks for your input, Heiko I found the likely cause in the source and have submitted a bug report (# 321). My impression is that the minimization itself is not affected. -Heiko __ Verschicken Sie SMS direkt vom Postfach aus - in alle deutschen und viele ausländische Netze zum gleichen Preis! https://produkte.web.de/webde_sms/sms ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error by pdb2gmx
Justin A. Lemkul wrote: Then it seems clear to me that your installation of Gromacs is faulty. Have you tried running the test set (available on the wiki site)? If you can describe your computer system (OS, version, compilers used, configuration options, etc.) then perhaps someone on the list can spot a potential pitfall. -Justin Yanmei Song wrote: Dear Justin: Thank you so much for your help earlier. I updated my GROMACS to 4.0.4. When I run pdb2gmx using the following two files. I still got the similar error message: Opening library file ffoplsaa.rtp Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading pdms2.pdb... Read 13 atoms Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 3 residues with 13 atoms chain #res #atoms 1 ' ' 3 13 All occupancies are one Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp --- Program pdb2gmx_d, VERSION 4.0.4 Source code file: resall.c, line: 279 Fatal error: in .rtp file at line: --- This error is being provoked at the top of the .rtp file when a line with something like [header] is not parsing suitably. A while ago I suggested using diff on the .rtp file. Do that. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
