<div> <br>Hi<br>6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs.<br>System = 6LYZ.pdb + CL- + water molecules<br> <br>Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all.<br>
Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Position restrained MD.<br> <br>The commands are as follows. <br>minim.mdp and pr.mdp are as follows.<br>And outputs are as follows.<br> <br>Any thing wrong?<br>
Thank you<br>Lin<br> <br> <br>=======================================================================================================<br> <br>- Hide quoted text -<br>grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated <br>
:-) G R O M A C S (-:<br> Good gRace! Old Maple Actually Chews Slate<br> :-) VERSION 4.0.5 (-:<br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org/">http://www.gromacs.org</a> for more information.<br>
This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br> :-) grompp_mpi (-:<br>Option Filename Type Description<br>------------------------------------------------------------<br>
-f minim.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br> -c 6LYZ-solvated.gro Input Structure file: gro g96 pdb tpr tpb tpa<br>
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -n index.ndx Input, Opt. Index file<br> -p 6LYZ.top Input Topology file<br>
-pp processed.top Output, Opt. Topology file<br> -o 6LYZ-EM-solvated.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br> -e ener.edr Input, Opt. Energy file: edr ene<br>
Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]v bool yes Be loud and noisy<br>
-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>-maxwarn int 0 Number of allowed warnings during input processing<br>
-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>-[no]renum bool yes Renumber atomtypes and minimize number of<br>
atomtypes<br>Ignoring obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp'<br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>checking input for internal consistency...<br>
processing topology...<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp<br>
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp<br>Generated 380 of the 1326 non-bonded parameter combinations<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp<br>Excluding 3 bonded neighbours molecule type 'Protein_A'<br>
Excluding 2 bonded neighbours molecule type 'SOL'<br>Excluding 1 bonded neighbours molecule type 'CL-'<br>processing coordinates...<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>
converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat<br>There are: 6512 OTHER residues<br>
There are: 129 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Protein...<br>Analysing Other...<br>Making dummy/rest group for T-Coupling containing 20841 elements<br>Making dummy/rest group for Acceleration containing 20841 elements<br>
Making dummy/rest group for Freeze containing 20841 elements<br>Making dummy/rest group for VCM containing 20841 elements<br>Number of degrees of freedom in T-Coupling group rest is 62520.00<br>Making dummy/rest group for User1 containing 20841 elements<br>
Making dummy/rest group for User2 containing 20841 elements<br>Making dummy/rest group for XTC containing 20841 elements<br>Making dummy/rest group for Or. Res. Fit containing 20841 elements<br>Making dummy/rest group for QMMM containing 20841 elements<br>
T-Coupling has 1 element(s): rest<br>Energy Mon. has 1 element(s): System<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>
NOTE 1 [file minim.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, which might produce artifacts.<br> You might want to consider using PME electrostatics.<br>This run will generate roughly 242 Mb of data<br>
writing run input file...<br>There was 1 note<br>Back Off! I just backed up 6LYZ-EM-solvated.tpr to ./#6LYZ-EM-solvated.tpr.1#<br>gcq#13: "If Life Seems Jolly Rotten, There's Something You've Forgotten !" (Monty Python)<br>
<br> <br> <br>=================================================================================================================<br> <br> grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr <br> :-) G R O M A C S (-:<br>
Giant Rising Ordinary Mutants for A Clerical Setup<br> :-) VERSION 4.0.5 (-:<br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org/">http://www.gromacs.org</a> for more information.<br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br> :-) grompp_mpi (-:<br>
Option Filename Type Description<br>------------------------------------------------------------<br> -f pr.mdp Input, Opt! grompp input file with MD parameters<br> -po mdout.mdp Output grompp input file with MD parameters<br>
-c 6LYZ-EM-solvated.gro Input Structure file: gro g96 pdb tpr tpb<br> tpa<br> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>
-n index.ndx Input, Opt. Index file<br> -p 6LYZ.top Input Topology file<br> -pp processed.top Output, Opt. Topology file<br> -o 6LYZ-PR.tpr Output Run input file: tpr tpb tpa<br> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br>
-e ener.edr Input, Opt. Energy file: edr ene<br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>
-[no]v bool yes Be loud and noisy<br>-time real -1 Take frame at or first after this time.<br>-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br> sites<br>
-maxwarn int 0 Number of allowed warnings during input processing<br>-[no]zero bool no Set parameters for bonded interactions without<br> defaults to zero instead of generating an error<br>
-[no]renum bool yes Renumber atomtypes and minimize number of<br> atomtypes<br>Ignoring obsolete mdp entry 'cpp'<br>Replacing old mdp entry 'unconstrained-start' by 'continuation'<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>checking input for internal consistency...<br>NOTE 1 [file pr.mdp, line unknown]:<br> The Berendsen thermostat does not generate the correct kinetic energy<br> distribution. You might want to consider using the V-rescale thermostat.<br>
processing topology...<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp<br>
Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp<br>Generated 380 of the 1326 non-bonded parameter combinations<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp<br>Excluding 3 bonded neighbours molecule type 'Protein_A'<br>
turning all bonds into constraints...<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>turning all bonds into constraints...<br>Excluding 1 bonded neighbours molecule type 'CL-'<br>turning all bonds into constraints...<br>
processing coordinates...<br>double-checking input for internal consistency...<br>Velocities were taken from a Maxwell distribution at 200 K<br>Reading position restraint coords from 6LYZ-EM-solvated.gro<br>renumbering atomtypes...<br>
converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat<br>There are: 6512 OTHER residues<br>
There are: 129 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Protein...<br>Analysing Other...<br>Making dummy/rest group for Acceleration containing 20841 elements<br>Making dummy/rest group for Freeze containing 20841 elements<br>
Making dummy/rest group for VCM containing 20841 elements<br>Number of degrees of freedom in T-Coupling group Protein is 2618.00<br>Number of degrees of freedom in T-Coupling group Non-Protein is 39048.00<br>Making dummy/rest group for User1 containing 20841 elements<br>
Making dummy/rest group for User2 containing 20841 elements<br>Making dummy/rest group for Or. Res. Fit containing 20841 elements<br>Making dummy/rest group for QMMM containing 20841 elements<br>T-Coupling has 2 element(s): Protein Non-Protein<br>
Energy Mon. has 2 element(s): Protein Non-Protein<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>XTC has 1 element(s): System<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>
This run will generate roughly 3 Mb of data<br>writing run input file...<br>There was 1 note<br>Back Off! I just backed up 6LYZ-PR.tpr to ./#6LYZ-PR.tpr.1#<br>gcq#52: "I'm a Wishbone and I'm Breaking" (Pixies)<br>
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<div>======================================================================================================<br>.out file<br> <br> <br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
1005 1006 41.4 0.1625 0.1078 0.1430<br> 1006 1007 30.6 0.1044 0.0899 0.1000<br> 1077 1081 129.5 0.2893 0.5930 0.1390<br> 1077 1078 102.3 0.0542 1.1847 0.1090<br>
1073 1077 167.5 1.0876 0.9651 0.1390<br> 1073 1076 57.2 0.6969 1.7573 0.1390<br> 1074 1076 63.8 0.6555 1.2119 0.1330<br> 1074 1075 101.0 1.3130 1.1709 0.1000<br>
1071 1074 108.5 1.0586 0.4070 0.1330<br> 1071 1072 94.2 0.6662 1.3755 0.1090<br> 1070 1071 114.1 0.6490 0.6753 0.1330<br> 1070 1073 155.5 1.0880 1.0783 0.1390<br>
1069 1070 78.1 0.2488 1.2798 0.1530</div>
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