[gmx-users] Solventbox equilibration
David van der Spoel
spoel at xray.bmc.uu.se
Mon May 22 19:00:59 CEST 2006
Anthony Cruz wrote:
> Hi:
> I have been trying to made a solvent box of methacrylic acid using parameters
> from PRODRG. I change it to GROMOS96 parameters and use charges from DFT
> calculation. I do the energy minimization with out any problem. I run a 2ns
> MD (NVT) with out any problem too. But when I try to run an MD (NPT) the
> process end with errors:
>
>
> :-) G R O M A C S (-:
>
> S C A M O R G
>
> :-) VERSION 3.3.1 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2006, 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 (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s MAA_BOX_MD2_PCOUPL_TPR.tpr Input Generic run input: tpr tpb tpa
> xml
> -o MAA_BOX_MD2_PCOUPL_MV.trr Output Full precision trajectory: trr
> trj
> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
> -c MAA_BOX_MD2_PCOUPL_CONF.gro Output Generic structure: gro g96 pdb
> xml
> -e MAA_BOX_MD2_PCOUPL_ENE.edr Output Generic energy: edr ene
> -g MAA_BOX_MD2_PCOUPL_LOG.log Output Log file
> -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
> -field field.xvg Output, Opt. xvgr/xmgr file
> -table table.xvg Input, Opt. xvgr/xmgr file
> -tablep tablep.xvg Input, Opt. xvgr/xmgr file
> -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
> -tpi tpi.xvg Output, Opt. xvgr/xmgr file
> -ei sam.edi Input, Opt. ED sampling input
> -eo sam.edo Output, Opt. ED sampling output
> -j wham.gct Input, Opt. General coupling stuff
> -jo bam.gct Output, Opt. General coupling stuff
> -ffout gct.xvg Output, Opt. xvgr/xmgr file
> -devout deviatie.xvg Output, Opt. xvgr/xmgr file
> -runav runaver.xvg Output, Opt. xvgr/xmgr file
> -pi pull.ppa Input, Opt. Pull parameters
> -po pullout.ppa Output, Opt. Pull parameters
> -pd pull.pdo Output, Opt. Pull data output
> -pn pull.ndx Input, Opt. Index file
> -mtx nm.mtx Output, Opt. Hessian matrix
> -dn dipole.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 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
> -np int 1 Number of nodes, must be the same as used for
> grompp
> -nt int 1 Number of threads to start on each node
> -[no]v bool yes Be loud and noisy
> -[no]compact bool yes Write a compact log file
> -[no]sepdvdl bool no Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -[no]multi bool no Do multiple simulations in parallel (only with
> -np > 1)
> -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 MAA_BOX_MD2_PCOUPL_LOG.log
> to ./#MAA_BOX_MD2_PCOUPL_LOG.log.3#
> Getting Loaded...
> Reading file MAA_BOX_MD2_PCOUPL_TPR.tpr, VERSION 3.3.1 (single precision)
> Loaded with Money
>
>
> Back Off! I just backed up MAA_BOX_MD2_PCOUPL_ENE.edr
> to ./#MAA_BOX_MD2_PCOUPL_ENE.edr.3#
> starting mdrun 'METHACRYLIC ACID BOX 200 MOLECULES'
> 3000000 steps, 3000.0 ps.
>
>
> Back Off! I just backed up MAA_BOX_MD2_PCOUPL_MV.trr
> to ./#MAA_BOX_MD2_PCOUPL_MV.trr.3#
> step 0
> Step 10 Warning: pressure scaling more than 1%, mu: 1.01929 1.01929 1.01929
> step 10, will finish at Thu May 25 15:12:22 2006
> Step 12 Warning: pressure scaling more than 1%, mu: 0.950214 0.950214
> 0.950214
>
> Step 13 Warning: pressure scaling more than 1%, mu: 1.06328 1.06328 1.06328
>
> Step 14 Warning: pressure scaling more than 1%, mu: 1.12283 1.12283 1.12283
>
> Step 15 Warning: pressure scaling more than 1%, mu: 0.75477 0.75477 0.75477
>
> Step 16 Warning: pressure scaling more than 1%, mu: 0.904104 0.904104
> 0.904104
>
> Step 17 Warning: pressure scaling more than 1%, mu: 2.56873 2.56873 2.56873
> Warning: 1-4 interaction between 99 and 104 at distance 1.007 which is larger
> than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
>
> Step 18 Warning: pressure scaling more than 1%, mu: 0.623727 0.623727
> 0.623727
>
> Step 18, time 0.018 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.910071 (between atoms 356 and 357) rms 1.093812
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 1 2 53.1 0.3937 0.1793 0.1530
> 2 3 50.9 0.3578 0.1601 0.1390
> 4 5 58.1 0.3168 0.0910 0.1230
> ...................
>
>
> What could be the problem? How I could resolve it????
check your topology.
use larger tau_p
>
>
> Anthony
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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