[gmx-users] problem with topology

[Maria Luisa]

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