<br><br><br>
Today's Topics:<br>
<br>
1. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken<br>
(Chih-Ying Lin)<br>
2. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output<br>
file) (Chih-Ying Lin)<br>
<br>
<br>
------------------------------<div id=":2g" class="ii gt">----------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 10 Jan 2010 10:11:17 +0800<br>
From: Chih-Ying Lin <<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>><br>
Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation<br>
Broken<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:5777f3841001091811l41fbe079ida9822609fc8e260@mail.gmail.com">5777f3841001091811l41fbe079ida9822609fc8e260@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi<br>
6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the<br>
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<br>
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>
1. Energy minimization of the structure (vacuum)<br>
pbc=no<br>
grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr<br>
mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum<br>
<br>
<br>
2. Periodic boundary conditions<br>
editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0<br>
6.0<br>
<br>
<br>
3. Solvent addition<br>
genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro<br>
<br>
<br>
4. Addition of ions: counter charge and concentration<br>
grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr<br>
genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL-<br>
<br>
<br>
5 Energy minimization of the solvated system => Potential Energy went to<br>
the very negative number<br>
pbc =xyz (minim.mdp)<br>
grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o<br>
6LYZ-EM-solvated<br>
mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated<br>
<br>
<br>
6 Relaxation of solvent and hydrogen atom positions: Position restrained<br>
MD => Simulation Broke<br>
grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr<br>
mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR<br>
<br>
<br>
=====================================================================================================<br>
minim.mdp<br>
<br>
; LINES STARTING WITH ';' ARE COMMENTS<br>
title = Minimization of Lysozyme (1LW9.pdb) ; Title of run<br>
; The following lines tell the program the standard locations where to<br>
find certain files<br>
cpp = /lib/cpp ; Preprocessor<br>
; Definea can be used to control processes<br>
define = -DFLEXIBLE<br>
; Parameters describing what to do, when to stop and what to save<br>
integrator = steep ; Algorithm (steep = steepest descent<br>
minimization)<br>
emtol = 1.0 ; Stop minimization when the maximum force <<br>
1.0 kJ/mol<br>
nsteps = 50000 ; Maximum number of (minimization) steps<br>
to perform<br>
nstenergy = 1 ; Write energies to disk every nstenergy<br>
steps<br>
energygrps = System ; Which energy group(s) to write to disk<br>
; Parameters describing how to find the neighbors of each atom and how to<br>
calculate the interactions<br>
nstlist = 5 ; Frequency to update the neighbor list<br>
and long range forces<br>
ns_type = simple ; Method to determine neighbor list<br>
(simple, grid)<br>
rlist = 1.0 ; Cut-off for making neighbor list (short<br>
range forces)<br>
coulombtype = cut-off ; Treatment of long range electrostatic<br>
interactions<br>
rcoulomb = 1.0 ; long range electrostatic cut-off<br>
rvdw = 1.0 ; long range Van der Waals cut-off<br>
constraints = none ; Bond types to replace by constraints<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
<br>
=================================================================================================<br>
pr.mdp<br>
<br>
; VARIOUS PREPROCESSING OPTIONS<br>
title =<br>
cpp = /lib/cpp<br>
include =<br>
define = -DPOSRES<br>
; RUN CONTROL PARAMETERS<br>
integrator = md<br>
tinit = 0<br>
dt = 0.001<br>
nsteps = 5000<br>
nstcomm = 0<br>
; OUTPUT CONTROL OPTIONS<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 1<br>
nstxtcout = 0<br>
xtc_precision = 1000<br>
xtc-grps = System<br>
energygrps = Protein Non-Protein<br>
; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 5<br>
ns-type = Grid<br>
pbc = xyz<br>
rlist = 0.9<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = Reaction-Field<br>
rcoulomb = 1.4<br>
epsilon_rf = 78<br>
epsilon_r = 1<br>
vdw-type = Cut-off<br>
rvdw = 1.4<br>
; Temperature coupling<br>
Tcoupl = Berendsen<br>
tc-grps = Protein Non-Protein<br>
tau_t = 0.1 0.1<br>
ref_t = 200 200<br>
; Pressure coupling<br>
Pcoupl = No<br>
; GENERATE VELOCITIES FOR STARTUP RUN<br>
gen_vel = yes<br>
gen_temp = 200.0<br>
gen_seed = 1735<br>
; OPTIONS FOR BONDS<br>
constraints = all-bonds<br>
constraint-algorithm = Lincs<br>
unconstrained-start = no<br>
lincs-order = 4<br>
lincs-iter = 1<br>
lincs-warnangle = 30<br>
<br>
<br>
<br>
<br>
<br>
<br>
=======================================================================================================<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Sun, 10 Jan 2010 10:29:35 +0800<br>
From: Chih-Ying Lin <<a href="mailto:chihying2008@gmail.com">chihying2008@gmail.com</a>><br>
Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation<br>
Broken (output file)<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:5777f3841001091829r4e88d83fs8eb680bb99077aa6@mail.gmail.com">5777f3841001091829r4e88d83fs8eb680bb99077aa6@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi<br>
6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the<br>
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<br>
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<br>
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/" target="_blank">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<br>
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<br>
./#6LYZ-EM-solvated.tpr.1#<br>
gcq#13: "If Life Seems Jolly Rotten, There's Something You've Forgotten !"<br>
(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/" target="_blank">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<br>
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>
<br>
<br>
<br>
====================================================================================================<br>
<br>
<br>
<br>
======================================================================================================<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<br><br><br><br></div><br>