[gmx-users] .top files

[Erik Lindahl]

Pedro Alexandre Lapido Loureiro wrote:

>
>Hello,
>
>After using the topol.top files of the DPPC benchmark, I was wondering:
>1)what is the meaning of "#define FF_GROMACS" ?
>

It just declares that we use the Gromacs forcefield. This way we can use 
topologies like spc.itp
for both Gromos96/Gromacs/OPLS-AA forcefields by checking for the define.

>
>2)the normal LJ interactions are not explicitly written in this top file, so the
>program must calculate C(6)ij and C(12)ij (and the 1-4 interactions,also, as
>long as generate pairs = yes).
>Suppose I want to use such an extended topology file for my own system: will
>this extra calculation deteriorate the performance of the program?
>
No, this is all done by grompp. When we process the topology we either 
look up or
calculate the 1,4 and normal LJ interactions for every possible pair of 
atomtypes (n.b., not atoms)
and store these in an array. It doesn't matter if we got the from an 
implicit combination rule
or by specifying the interactions explicitly.

The only thing that can deteriorate performance is if you actually USE 
hundreds or thousands
of different atomtypes in a system (it won't hurt to just have them 
declared as in OPLS - any normal
simulation will only use a small fraction of them).


Cheers,

Erik