Hello,
Here I am sending the complete output after the md.csh command with the
errors in bold.
COMMAND: csh md.csh
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) 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 (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f md-md.mdp Input, Opt! grompp input file with MD parameters
-po inmd.mdp Output grompp input file with MD parameters
-c results/eq1bar300K.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_sol.ndx Input, Opt! Index file
-p topol_sol_hbond_131210.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o inmd.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
*ERROR
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: statutil.c, line: 727
Invalid command line argument:
-------------------------------------------------------*
Thanx for Using GROMACS - Have a Nice Day
[1] 16658
: Command not found.
:-) G R O M A C S (-:
Great Red Oystrich Makes All Chemists Sane
:-) 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.
:-) mdrun (double precision) (-:
achje05
(/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210)>
Option Filename Type Description
------------------------------------------------------------
-s inmd.tpr Input Run input file: tpr tpb tpa
-o MDResults/md.trr Output Full precision trajectory: trr trj cpt
-x MDResults/md.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi MDResults/md.cpt Input, Opt. Checkpoint file
-cpo MDResults/md.cpt Output, Opt. Checkpoint file
-c MDResults/md.gro Output Structure file: gro g96 pdb
-e MDResults/md.edr Output Energy file: edr ene
-g MDResults/md.log Output Log file
-dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr file
-field MDResults/md.xvg Output, Opt. xvgr/xmgr file
-table MDResults/md.xvg Input, Opt. xvgr/xmgr file
-tablep MDResults/md.xvg Input, Opt. xvgr/xmgr file
-tableb MDResults/md.xvg Input, Opt. xvgr/xmgr file
-rerun MDResults/md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb
cpt
-tpi MDResults/md.xvg Output, Opt. xvgr/xmgr file
-tpid MDResults/md.xvg Output, Opt. xvgr/xmgr file
-ei MDResults/md.edi Input, Opt. ED sampling input
-eo MDResults/md.edo Output, Opt. ED sampling output
-j MDResults/md.gct Input, Opt. General coupling stuff
-jo MDResults/md.gct Output, Opt. General coupling stuff
-ffout MDResults/md.xvg Output, Opt. xvgr/xmgr file
-devout MDResults/md.xvg Output, Opt. xvgr/xmgr file
-runav MDResults/md.xvg Output, Opt. xvgr/xmgr file
-px MDResults/md.xvg Output, Opt. xvgr/xmgr file
-pf MDResults/md.xvg Output, Opt. xvgr/xmgr file
-mtx MDResults/md.mtx Output, Opt. Hessian matrix
-dn MDResults/md.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string MDResults/md Set the default filename for all file
options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or
cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions
with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or
yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-[no]sum bool yes Sum the energies at every step
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]append bool no Append to previous output files when continuing
from checkpoint
-[no]addpart bool yes Add the simulation part number to all output
files when continuing from checkpoint
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up MDResults/md.log to MDResults/#md.log.3#
*ERROR
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: gmxfio.c, line: 736
Can not open file:
inmd.tpr
-------------------------------------------------------*
"And You Will Know That My Name is the Lord When I Lay My Vengeance Upon
Thee." (Pulp Fiction)
yours sincerely,
uday.
On Tue, Dec 14, 2010 at 11:05 AM, Sarath Chandra <
sarathchandrada...@gmail.com> wrote:
>
>
> On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran <kiran.ud...@gmail.com>wrote:
>
>> Hello madam,
>>
>> The command id
>>
>> *csh* *md.csh
>>
>> *
>
>
> Please paste your md.csh file and the error you get in detail.
>
>
>> **As I see, there is no error in the command. All other commands are
>> properly working (like eq.csh, em.csh etc ). The problem is only with
>> md.csh.
>>
>> yours sincerely,
>> uday.
>>
>> --
>> 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/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>>
>
>
> Best Wishes,
>
>
> Sarath
>
--
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