[gmx-users] .top files

[Erik Lindahl]

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:
>  
>
Hi,

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