The input to your grompp command is wrong. You have selected an invalid grompp option. Please verify the grompp command and rerun the script.<br><br><div class="gmail_quote">On Tue, Dec 14, 2010 at 11:13 AM, udaya kiran <span dir="ltr"><<a href="mailto:kiran.udaya@gmail.com">kiran.udaya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hello,<br><br>Here I am sending the complete output after the md.csh command with the errors in bold.<br>
<br><br>COMMAND: csh md.csh
<br> <br> <br> :-) G R O M A C S (-:
<br> <br> Groningen Machine for Chemical Simulation
<br> <br> :-) VERSION 4.0.5 (-:
<br> <br> <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> <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> <br> :-) grompp (double precision) (-:
<br> <br>Option Filename Type Description
<br>------------------------------------------------------------
<br> -f md-md.mdp Input, Opt! grompp input file with MD parameters
<br> -po inmd.mdp Output grompp input file with MD parameters
<br> -c results/eq1bar300K.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_sol.ndx Input, Opt! Index file
<br> -p topol_sol_hbond_131210.top Input Topology file
<br> -pp processed.top Output, Opt. Topology file
<br> -o inmd.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> <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> <br><b>ERROR
<br>-------------------------------------------------------
<br>Program grompp, VERSION 4.0.5
<br>Source code file: statutil.c, line: 727
<br> <br>Invalid command line argument:
<br> <br>-------------------------------------------------------</b>
<br> <br>Thanx for Using GROMACS - Have a Nice Day
<br> <br>[1] 16658
<br>: Command not found.
<br> :-) G R O M A C S (-:
<br> <br> Great Red Oystrich Makes All Chemists Sane
<br> <br> :-) VERSION 4.0.5 (-:
<br> <br> <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> <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> <br> :-) mdrun (double precision) (-:
<br> <br>achje05 (/loch/akbl1/marelli/PROJECTS/16L4_16_aAALAA/16L4_GROMACS_RUN_HB3_131210)> Option Filename Type Description
<br>------------------------------------------------------------
<br> -s inmd.tpr Input Run input file: tpr tpb tpa
<br> -o MDResults/md.trr Output Full precision trajectory: trr trj cpt
<br> -x MDResults/md.xtc Output, Opt. Compressed trajectory (portable xdr
<br> format)
<br>-cpi MDResults/md.cpt Input, Opt. Checkpoint file
<br>-cpo MDResults/md.cpt Output, Opt. Checkpoint file
<br> -c MDResults/md.gro Output Structure file: gro g96 pdb
<br> -e MDResults/md.edr Output Energy file: edr ene
<br> -g MDResults/md.log Output Log file
<br>-dgdl MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br>-field MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br>-table MDResults/md.xvg Input, Opt. xvgr/xmgr file
<br>-tablep MDResults/md.xvg Input, Opt. xvgr/xmgr file
<br>-tableb MDResults/md.xvg Input, Opt. xvgr/xmgr file
<br>-rerun MDResults/md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
<br>-tpi MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br>-tpid MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br> -ei MDResults/md.edi Input, Opt. ED sampling input
<br> -eo MDResults/md.edo Output, Opt. ED sampling output
<br> -j MDResults/md.gct Input, Opt. General coupling stuff
<br> -jo MDResults/md.gct Output, Opt. General coupling stuff
<br>-ffout MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br>-devout MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br>-runav MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br> -px MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br> -pf MDResults/md.xvg Output, Opt. xvgr/xmgr file
<br>-mtx MDResults/md.mtx Output, Opt. Hessian matrix
<br> -dn MDResults/md.ndx Output, Opt. Index file
<br> <br>Option Type Value Description
<br>------------------------------------------------------
<br>-[no]h bool no Print help info and quit
<br>-nice int 19 Set the nicelevel
<br>-deffnm string MDResults/md Set the default filename for all file
<br> options
<br>-[no]xvgr bool yes Add specific codes (legends etc.) in the output
<br> xvg files for the xmgrace program
<br>-[no]pd bool no Use particle decompostion
<br>-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
<br>-npme int -1 Number of separate nodes to be used for PME, -1
<br> is guess
<br>-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
<br>-[no]ddcheck bool yes Check for all bonded interactions with DD
<br>-rdd real 0 The maximum distance for bonded interactions with
<br> DD (nm), 0 is determine from initial coordinates
<br>-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
<br>-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
<br>-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
<br>-[no]sum bool yes Sum the energies at every step
<br>-[no]v bool no Be loud and noisy
<br>-[no]compact bool yes Write a compact log file
<br>-[no]seppot bool no Write separate V and dVdl terms for each
<br> interaction type and node to the log file(s)
<br>-pforce real -1 Print all forces larger than this (kJ/mol nm)
<br>-[no]reprod bool no Try to avoid optimizations that affect binary
<br> reproducibility
<br>-cpt real 15 Checkpoint interval (minutes)
<br>-[no]append bool no Append to previous output files when continuing
<br> from checkpoint
<br>-[no]addpart bool yes Add the simulation part number to all output
<br> files when continuing from checkpoint
<br>-maxh real -1 Terminate after 0.99 times this time (hours)
<br>-multi int 0 Do multiple simulations in parallel
<br>-replex int 0 Attempt replica exchange every # steps
<br>-reseed int -1 Seed for replica exchange, -1 is generate a seed
<br>-[no]glas bool no Do glass simulation with special long range
<br> corrections
<br>-[no]ionize bool no Do a simulation including the effect of an X-Ray
<br> bombardment on your system
<br> <br> <br>Back Off! I just backed up MDResults/md.log to MDResults/#md.log.3#
<br> <br><b>ERROR
<br>-------------------------------------------------------
<br>Program mdrun, VERSION 4.0.5
<br>Source code file: gmxfio.c, line: 736
<br> <br>Can not open file:
<br>inmd.tpr
<br>-------------------------------------------------------</b>
<br> <br>"And You Will Know That My Name is the Lord When I Lay My Vengeance Upon Thee." (Pulp Fiction)
<br><br><br><br><br>yours sincerely,<br>uday.<div><div></div><div class="h5"><br><br><br><div class="gmail_quote">On Tue, Dec 14, 2010 at 11:05 AM, Sarath Chandra <span dir="ltr"><<a href="mailto:sarathchandradantu@gmail.com" target="_blank">sarathchandradantu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><br><div class="gmail_quote"><div>On Tue, Dec 14, 2010 at 10:07 AM, udaya kiran <span dir="ltr"><<a href="mailto:kiran.udaya@gmail.com" target="_blank">kiran.udaya@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello madam,<br><br>The command id <br><br><i>csh</i> <i>md.csh<br><br></i></blockquote></div><div><br>Please paste your md.csh file and the error you get in detail.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<i></i>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.<br>
<br>yours sincerely,<br>uday.<br>
<br></div>--<br>
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