[gmx-users] problem with topology

Dallas Warren dallas.warren at monash.edu
Tue Jun 11 11:48:53 CEST 2019

Do you have a .itp for each molecule? How did you generate the box with the
multiple molecules? What is the contents of your .top file? What was the
exact commands you used? What was the exact output? Copy and paste, do not
type out what you think it says.

Suspect there may be a problem with how you are calling the topology.

On Tue, 11 Jun. 2019, 6:32 pm Maria Luisa, <ml.perrotta at itm.cnr.it> wrote:

> Dear user.
> I have a problem. I have to simulate a box of 100 molecules of
> polyvinylidene fluoride (PVDF) and 1436 molecules of the solvent ATBC. At
> first I built the single chain of PVDf and a single molecules of ATBC, and
> I was able to construct topology using opls force-field. The command that
> I used is gmx x2top. When I create the complete box with a total amount of
> 95320 atoms, an error occurs saying to me that it's possible recognize
> only 1800 atoms of 95320. This is strange, because the two molecules are
> written in the topology file each one, but not together in the box. What
> is the problem? Is there some bug with my version of gromacs (5.1.4)?
> I wait for your answer
> Maria Luisa
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perrotta at itm.cnr.it
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