[gmx-users] min in vacuum

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Wed Jun 18 11:08:50 CEST 2014

Hi gromacs users,

I am trying to run coarse-grained MD for a protein system  using martini
protocol. First step is to run short min in vacuum, whenever I try to do
this I am getting an error regarding my input file.

 ERROR 1 [file system-vaccum.top, line 16]:
  ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rlist.

There was 1 note

Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1356

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"I Caught It In the Face" (P.J. Harvey)

My input file:

integrator       =  steep
dt               =  0.02
nsteps           =  10
nstxout          =  0
nstvout          =  0
nstlog           =  100
nstxtcout        =  100
xtc-precision    =  10
rlist            =  1.4
coulombtype      =  shift
rcoulomb         =  1.2
epsilon_r        =  15
vdw-type         =  shift
rvdw-switch      =  0.9
rvdw             =  1.2
tcoupl           =  v-rescale
tc-grps          =  Protein
tau-t            =  1.0
ref-t            =  300

How should I modify it?

Thank you in advance for any suggestions.
best regards

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