[gmx-users] get a top file to run md simulation

oguz gurbulak gurbulakoguz at yahoo.com
Fri Mar 13 15:17:49 CET 2009

Dear Users,

I'm trying
to obtain .gro and top files successfuly for my n-alkanes molecules and
want to run md simulations both using oplsaa and Gromos96 force fields
seperately. Then I will compare the results of two md runs. I think
that I can generate itp files for Gromos96 force fields  using prodgr
server and use them for md. But I sholud  write itp files for each
molecules I want to use for oplsaa . Lets say that I produced itp
files, How can I use for example two different itp files and generate a
top file like in below. I'm confused about this. Could you give me the information about this
procedure ?


#include "ffoplsaa.itp"

#include "molecule_A.itp"
#include "molecule_B.itp"

[ system ]
packmol system

[ molecules ]
Molecule_B    N

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