[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken
Chih-Ying Lin
chihying2008 at gmail.com
Mon Jan 11 20:11:39 CET 2010
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 <chihying2008 at gmail.com>
Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation
Broken
To: gmx-users at gromacs.org
Message-ID:
<5777f3841001091811l41fbe079ida9822609fc8e260 at mail.gmail.com>
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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
=======================================================================================================
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Message: 2
Date: Sun, 10 Jan 2010 10:29:35 +0800
From: Chih-Ying Lin <chihying2008 at gmail.com>
Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation
Broken (output file)
To: gmx-users at gromacs.org
Message-ID:
<5777f3841001091829r4e88d83fs8eb680bb99077aa6 at 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
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