[gmx-users] .top files

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Thu Oct 31 20:40:52 CET 2002

> The [ moleculetype ] directive is used to define a single molecule, so you
> should have one for DPPC, and then [ atoms ], [ bonds ], etc for the 
> DPPC molcule.
> After that, you can have a new [moleculetype] for HAL, with all section for
> this molecule.
> Finally (at the very end) you have a [ system ] and then a [ molecules ] 
> section specifying
> how many molecules of each sort are present in the system.
> I prefer to separate forcefields from molecule definitions, so that I 
> can just #include the
> forcefield and the molecules I need in each simulation, but that's a 
> matter of taste.
> Cheers,
> Erik
 Thanks, Erik: it runs smoothly now!!
By the way, the main reference for this forcefield would be
"W. Jorgensen & J Tirado-Rives, J Am Chem Soc 110, 1657 (1988)" ?

Cheers, Pedro. 

Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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