On 4/27/2011 6:21 AM, delara aghaie wrote:
Dear Gromacs users
I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg
and 16 Cl ions using genion and now want to use grompp and then start
the simulation to see the effect of ions on the pressure-area isotherm
of the system.
running grompp in gromacs 3.3 I see he following error:
Unless you have an important reason of continuity for using GROMACS 3.3,
you will get much better performance from the latest GROMACS version.
Mark
please help em to solve it.let me knoe please what is cpp?
Thanks in advance
D. Aghaie
-bash-3.2$ grompp_mpi -c dppc-salt-Mg-0.1.gro -f run.mdp -n
indexsalt-Mg.ndx -p topoldppc.top -o topol.tpr -np 8
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.orgfor 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 run.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c dppc-salt-Mg-0.1.gro Input Generic structure: gro g96 pdb tpr
tpb tpa xml
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr
tpb tpa
xml
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr
tpb tpa
xml
-n indexsalt-Mg.ndx Input, Opt! Index file
-deshuf deshuf.ndx Output, Opt. Index file
-p topoldppc.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Generic run input: tpr tpb tpa xml
-t traj.trr Input, Opt. Full precision trajectory: trr trj
-e ener.edr Input, Opt. Generic energy: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line
options
-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.
-np int 8 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
-[no]rmvsbds bool yes Remove constant bonded interactions with
virtual
sites
-load string Releative load capacity of each node on a
parallel machine. Be sure to use quotes around
the string, which should contain a number for
each node
-maxwarn int 10 Number of warnings after which input
processing
stops
-[no]check14 bool no Remove 1-4 interactions without Van der Waals
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
creating statusfile for 8 nodes...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling cpp...
topoldppc.top:7:20: error: ions.itp: No such file or directory
cpp exit code: 256
Tried to execute: 'cpp -I/apps/gromacs/3.3/share/top topoldppc.top >
gromppzVWhWp'
The 'cpp' command is defined in the .mdp file
processing topology...
Generated 1369 of the 2211 non-bonded parameter combinations
Excluding 3 bonded neighbours for DPP 64
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 4152
turning all bonds into constraints...
Cleaning up temporary file gromppzVWhWp
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3
Source code file: toppush.c, line: 1264
Fatal error:
No such moleculetype Mg
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
--
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