Now try hard to resist running on multiple processors... Tsjerk
On Mon, Jan 11, 2010 at 8:11 PM, Chih-Ying Lin <chihying2...@gmail.com> wrote: > > > > Today's Topics: > > 1. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken > (Chih-Ying Lin) > 2. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output > file) (Chih-Ying Lin) > > > ------------------------------ > ---------------------------------------- > > Message: 1 > Date: Sun, 10 Jan 2010 10:11:17 +0800 > From: Chih-Ying Lin <chihying2...@gmail.com> > Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation > Broken > To: gmx-users@gromacs.org > Message-ID: > <5777f3841001091811l41fbe079ida9822609fc8e...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi > 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the > simulation on Gromacs. > System = 6LYZ.pdb + CL- + water molecules > > Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. > Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step > Position restrained MD. > > The commands are as follows. > minim.mdp and pr.mdp are as follows. > And outputs are as follows. > > Any thing wrong? > Thank you > Lin > > > 1. Energy minimization of the structure (vacuum) > pbc=no > grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr > mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum > > > 2. Periodic boundary conditions > editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0 > 6.0 > > > 3. Solvent addition > genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro > > > 4. Addition of ions: counter charge and concentration > grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr > genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL- > > > 5 Energy minimization of the solvated system => Potential Energy went to > the very negative number > pbc =xyz (minim.mdp) > grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o > 6LYZ-EM-solvated > mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated > > > 6 Relaxation of solvent and hydrogen atom positions: Position restrained > MD => Simulation Broke > grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr > mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR > > > ===================================================================================================== > minim.mdp > > ; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization of Lysozyme (1LW9.pdb) ; Title of run > ; The following lines tell the program the standard locations where to > find certain files > cpp = /lib/cpp ; Preprocessor > ; Definea can be used to control processes > define = -DFLEXIBLE > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1.0 ; Stop minimization when the maximum force < > 1.0 kJ/mol > nsteps = 50000 ; Maximum number of (minimization) steps > to perform > nstenergy = 1 ; Write energies to disk every nstenergy > steps > energygrps = System ; Which energy group(s) to write to disk > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 5 ; Frequency to update the neighbor list > and long range forces > ns_type = simple ; Method to determine neighbor list > (simple, grid) > rlist = 1.0 ; Cut-off for making neighbor list (short > range forces) > coulombtype = cut-off ; Treatment of long range electrostatic > interactions > rcoulomb = 1.0 ; long range electrostatic cut-off > rvdw = 1.0 ; long range Van der Waals cut-off > constraints = none ; Bond types to replace by constraints > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > ================================================================================================= > pr.mdp > > ; VARIOUS PREPROCESSING OPTIONS > title = > cpp = /lib/cpp > include = > define = -DPOSRES > ; RUN CONTROL PARAMETERS > integrator = md > tinit = 0 > dt = 0.001 > nsteps = 5000 > nstcomm = 0 > ; OUTPUT CONTROL OPTIONS > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 10 > nstenergy = 1 > nstxtcout = 0 > xtc_precision = 1000 > xtc-grps = System > energygrps = Protein Non-Protein > ; NEIGHBORSEARCHING PARAMETERS > nstlist = 5 > ns-type = Grid > pbc = xyz > rlist = 0.9 > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = Reaction-Field > rcoulomb = 1.4 > epsilon_rf = 78 > epsilon_r = 1 > vdw-type = Cut-off > rvdw = 1.4 > ; Temperature coupling > Tcoupl = Berendsen > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 200 200 > ; Pressure coupling > Pcoupl = No > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp = 200.0 > gen_seed = 1735 > ; OPTIONS FOR BONDS > constraints = all-bonds > constraint-algorithm = Lincs > unconstrained-start = no > lincs-order = 4 > lincs-iter = 1 > lincs-warnangle = 30 > > > > > > > ======================================================================================================= > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100110/8934cb36/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sun, 10 Jan 2010 10:29:35 +0800 > From: Chih-Ying Lin <chihying2...@gmail.com> > Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation > Broken (output file) > To: gmx-users@gromacs.org > Message-ID: > <5777f3841001091829r4e88d83fs8eb680bb99077...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi > 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the > simulation on Gromacs. > System = 6LYZ.pdb + CL- + water molecules > > Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. > Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step > Position restrained MD. > > The commands are as follows. > minim.mdp and pr.mdp are as follows. > And outputs are as follows. > > Any thing wrong? > Thank you > Lin > > > ======================================================================================================= > > - Hide quoted text - > grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o > 6LYZ-EM-solvated > :-) G R O M A C S (-: > Good gRace! Old Maple Actually Chews Slate > :-) VERSION 4.0.5 (-: > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, The GROMACS development team, > 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. > :-) grompp_mpi (-: > Option Filename Type Description > ------------------------------------------------------------ > -f minim.mdp Input, Opt! grompp input file with MD parameters > -po mdout.mdp Output grompp input file with MD parameters > -c 6LYZ-solvated.gro Input Structure file: gro g96 pdb tpr tpb tpa > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -n index.ndx Input, Opt. Index file > -p 6LYZ.top Input Topology file > -pp processed.top Output, Opt. Topology file > -o 6LYZ-EM-solvated.tpr Output Run input file: tpr tpb tpa > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt > -e ener.edr Input, Opt. Energy file: edr ene > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -nice int 0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with virtual > sites > -maxwarn int 0 Number of allowed warnings during input > processing > -[no]zero bool no Set parameters for bonded interactions without > defaults to zero instead of generating an error > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > Ignoring obsolete mdp entry 'title' > Ignoring obsolete mdp entry 'cpp' > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# > checking input for internal consistency... > processing topology... > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp > Generated 380 of the 1326 non-bonded parameter combinations > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp > Excluding 3 bonded neighbours molecule type 'Protein_A' > Excluding 2 bonded neighbours molecule type 'SOL' > Excluding 1 bonded neighbours molecule type 'CL-' > processing coordinates... > double-checking input for internal consistency... > renumbering atomtypes... > converting bonded parameters... > initialising group options... > processing index file... > Analysing residue names: > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat > There are: 6512 OTHER residues > There are: 129 PROTEIN residues > There are: 0 DNA residues > Analysing Protein... > Analysing Other... > Making dummy/rest group for T-Coupling containing 20841 elements > Making dummy/rest group for Acceleration containing 20841 elements > Making dummy/rest group for Freeze containing 20841 elements > Making dummy/rest group for VCM containing 20841 elements > Number of degrees of freedom in T-Coupling group rest is 62520.00 > Making dummy/rest group for User1 containing 20841 elements > Making dummy/rest group for User2 containing 20841 elements > Making dummy/rest group for XTC containing 20841 elements > Making dummy/rest group for Or. Res. Fit containing 20841 elements > Making dummy/rest group for QMMM containing 20841 elements > T-Coupling has 1 element(s): rest > Energy Mon. has 1 element(s): System > Acceleration has 1 element(s): rest > Freeze has 1 element(s): rest > User1 has 1 element(s): rest > User2 has 1 element(s): rest > VCM has 1 element(s): rest > XTC has 1 element(s): rest > Or. Res. Fit has 1 element(s): rest > QMMM has 1 element(s): rest > Checking consistency between energy and charge groups... > NOTE 1 [file minim.mdp, line unknown]: > You are using a plain Coulomb cut-off, which might produce artifacts. > You might want to consider using PME electrostatics. > This run will generate roughly 242 Mb of data > writing run input file... > There was 1 note > Back Off! I just backed up 6LYZ-EM-solvated.tpr to > ./#6LYZ-EM-solvated.tpr.1# > gcq#13: "If Life Seems Jolly Rotten, There's Something You've Forgotten !" > (Monty Python) > > > > ================================================================================================================= > > grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr > :-) G R O M A C S (-: > Giant Rising Ordinary Mutants for A Clerical Setup > :-) VERSION 4.0.5 (-: > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, The GROMACS development team, > 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. > :-) grompp_mpi (-: > Option Filename Type Description > ------------------------------------------------------------ > -f pr.mdp Input, Opt! grompp input file with MD parameters > -po mdout.mdp Output grompp input file with MD parameters > -c 6LYZ-EM-solvated.gro Input Structure file: gro g96 pdb tpr tpb > tpa > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -n index.ndx Input, Opt. Index file > -p 6LYZ.top Input Topology file > -pp processed.top Output, Opt. Topology file > -o 6LYZ-PR.tpr Output Run input file: tpr tpb tpa > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt > -e ener.edr Input, Opt. Energy file: edr ene > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -nice int 0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with virtual > sites > -maxwarn int 0 Number of allowed warnings during input > processing > -[no]zero bool no Set parameters for bonded interactions without > defaults to zero instead of generating an error > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > Ignoring obsolete mdp entry 'cpp' > Replacing old mdp entry 'unconstrained-start' by 'continuation' > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# > checking input for internal consistency... > NOTE 1 [file pr.mdp, line unknown]: > The Berendsen thermostat does not generate the correct kinetic energy > distribution. You might want to consider using the V-rescale thermostat. > processing topology... > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp > Generated 380 of the 1326 non-bonded parameter combinations > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp > Excluding 3 bonded neighbours molecule type 'Protein_A' > turning all bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'CL-' > turning all bonds into constraints... > processing coordinates... > double-checking input for internal consistency... > Velocities were taken from a Maxwell distribution at 200 K > Reading position restraint coords from 6LYZ-EM-solvated.gro > renumbering atomtypes... > converting bonded parameters... > initialising group options... > processing index file... > Analysing residue names: > Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat > There are: 6512 OTHER residues > There are: 129 PROTEIN residues > There are: 0 DNA residues > Analysing Protein... > Analysing Other... > Making dummy/rest group for Acceleration containing 20841 elements > Making dummy/rest group for Freeze containing 20841 elements > Making dummy/rest group for VCM containing 20841 elements > Number of degrees of freedom in T-Coupling group Protein is 2618.00 > Number of degrees of freedom in T-Coupling group Non-Protein is 39048.00 > Making dummy/rest group for User1 containing 20841 elements > Making dummy/rest group for User2 containing 20841 elements > Making dummy/rest group for Or. Res. Fit containing 20841 elements > Making dummy/rest group for QMMM containing 20841 elements > T-Coupling has 2 element(s): Protein Non-Protein > Energy Mon. has 2 element(s): Protein Non-Protein > Acceleration has 1 element(s): rest > Freeze has 1 element(s): rest > User1 has 1 element(s): rest > User2 has 1 element(s): rest > VCM has 1 element(s): rest > XTC has 1 element(s): System > Or. Res. Fit has 1 element(s): rest > QMMM has 1 element(s): rest > Checking consistency between energy and charge groups... > This run will generate roughly 3 Mb of data > writing run input file... > There was 1 note > Back Off! I just backed up 6LYZ-PR.tpr to ./#6LYZ-PR.tpr.1# > gcq#52: "I'm a Wishbone and I'm Breaking" (Pixies) > > > > ==================================================================================================== > > > > ====================================================================================================== > .out file > > > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1005 1006 41.4 0.1625 0.1078 0.1430 > 1006 1007 30.6 0.1044 0.0899 0.1000 > 1077 1081 129.5 0.2893 0.5930 0.1390 > 1077 1078 102.3 0.0542 1.1847 0.1090 > 1073 1077 167.5 1.0876 0.9651 0.1390 > 1073 1076 57.2 0.6969 1.7573 0.1390 > 1074 1076 63.8 0.6555 1.2119 0.1330 > 1074 1075 101.0 1.3130 1.1709 0.1000 > 1071 1074 108.5 1.0586 0.4070 0.1330 > 1071 1072 94.2 0.6662 1.3755 0.1090 > 1070 1071 114.1 0.6490 0.6753 0.1330 > 1070 1073 155.5 1.0880 1.0783 0.1390 > 1069 1070 78.1 0.2488 1.2798 0.1530 > > > > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
