[gmx-users] min in vacuum

[Justin Lemkul]

On 6/18/14, 5:08 AM, Urszula Uciechowska wrote:
> 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?
>

Probably your box is too small.  You haven't set the "pbc" keyword, so it 
defaults to "xyz," which is not really a vacuum system and will cause problems 
if the box is not of sufficient size.  Note that the temperature settings and dt 
are ignored for EM.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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