sakthi kumaran wrote:
Sorry. I will make my statements clear here after.
here is the terminal output after executing grompp -v
:-) G R O M A C S (-:
Great Red Oystrich Makes All Chemists Sane
:-) VERSION 4.0.7 (-:
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 <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 (-:
Option Filename Type Description
------------------------------------------------------------
-f grompp.mdp Input, Opt. grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c conf.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 topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.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'
Ignoring obsolete mdp entry 'domain-decomposition'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Ignoring obsolete mdp entry 'dihre-tau'
Ignoring obsolete mdp entry 'nstdihreout'
Ignoring obsolete mdp entry 'nstcheckpoint'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
WARNING 1 [file grompp.mdp, line unknown]:
Unknown or double left-hand 'bd-temp' in parameter file
checking input for internal consistency...
NOTE 1 [file grompp.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/share/gromacs/top/ffgmx.itp
Opening library file /usr/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/share/gromacs/top/ff_dum.itp
Opening library file /usr/share/gromacs/top/spc.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/share/gromacs/top/aminoacids.dat
There are: 216 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
Making dummy/rest group for Acceleration containing 648 elements
Making dummy/rest group for Freeze containing 648 elements
Making dummy/rest group for Energy Mon. containing 648 elements
Making dummy/rest group for VCM containing 648 elements
Number of degrees of freedom in T-Coupling group System is 1293.00
Making dummy/rest group for User1 containing 648 elements
Making dummy/rest group for User2 containing 648 elements
Making dummy/rest group for XTC containing 648 elements
Making dummy/rest group for Or. Res. Fit containing 648 elements
Making dummy/rest group for QMMM containing 648 elements
T-Coupling has 1 element(s): System
Energy Mon. has 1 element(s): rest
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 2 [file grompp.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 1 Mb of data
writing run input file...
There were 2 notes
There was 1 warning
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------
"And You Will Know That My Name is the Lord When I Lay My Vengeance Upon
Thee." (Pulp Fiction)
Please make note of the big, bold WARNING a few lines up. This is the cause of
the fatal error. As I warned you before, some of the demo files are outdated
and will not work. There is far more tutorial material available from the
Gromacs site that (I think) is more instructive than the simple examples
provided as part of the demo. Unfortunately, it appears that the Gromacs site
is down, so you won't be able to access all of the tutorial material, so either
wait for the site to come back up or fix the .mdp file so that it contains
sensible parameters.
-Justin
*after executing gmxdump the error is *
**
gmxdump -s topol.tpr | more
:-) G R O M A C S (-:
Go Rough, Oppose Many Angry Chinese Serial killers
:-) VERSION 4.0.7 (-:
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 <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.
:-) gmxdump (-:
Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input, Opt! Run input file: tpr tpb tpa
-f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-e ener.edr Input, Opt. Energy file: edr ene
-cp state.cpt Input, Opt. Checkpoint file
-p topol.top Input, Opt. Topology file
-mtx hessian.mtx Input, Opt. Hessian matrix
-om grompp.mdp Output, Opt. grompp input file with MD parameters
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]nr bool yes Show index numbers in output (leaving them out
makes comparison easier, but creates a useless
topology)
-[no]sys bool no List the atoms and bonded interactions for the
whole system instead of for each molecule type
-------------------------------------------------------
Program gmxdump, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737
Can not open file:
topol.tpr
-------------------------------------------------------
"I Need Love, Not Games" (Iggy Pop & Kate Pierson)
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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