[gmx-users] Solventbox equilibration

Anthony Cruz acb15885 at uprm.edu
Mon May 22 19:00:40 CEST 2006

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
  -o MAA_BOX_MD2_PCOUPL_MV.trr  Output       Full precision trajectory: trr
  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
  -c MAA_BOX_MD2_PCOUPL_CONF.gro  Output       Generic structure: gro g96 pdb
  -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
         -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
 -[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#
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 

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 

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 

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????


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