[gmx-users] .top files

Erik Lindahl lindahl at stanford.edu
Thu Oct 31 19:44:37 CET 2002

Pedro Alexandre Lapido Loureiro wrote:

>Thank you Erik and Marcos for your answers, but I am still a bit confused.
>If you don't mind, I will send you a short version of my .top file:

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.



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