[gmx-users] Topol file for a bigger system

Justin Lemkul jalemkul at vt.edu
Tue Mar 20 01:57:29 CET 2018

On 3/19/18 8:15 PM, Alex wrote:
> Dear all,
> Using topolbuild I can generate the case.gro, case.top, ffcase.itp and
> posrecase.itp out of a case.mol2 which contain only a single molecule of X.
> Also, using the "gmx insert-molecules" I can generate a bigger system
> containing 1000 molecule of X, for example to have case-1000.gro.
> Now, I was wondering how I can update the case.top and itp files for the
> new system? I am trying the "gmx x2top" but first of all it is really time
> consuming and also at the end it can not find the force fields for some of
> the atoms.
> (~> gmx x2top -f case-1000.gro -o out.top -r out.rtp)

Shouldn't it be as simple as updating the number of molecules in the 
.top file to 1000?

There are no changes in .itp files, as only a .top keeps record of how 
many of each species there are.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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