[gmx-users] questions on topology files

[Erik Lindahl]

Hi David,

>
>
> 1) In ffG43a1nb.itp there is a field know as p-type under the section
> [atomtypes] whose value is typically “A”.  What is this value?

The particle type. 'A' means atom, and that's the only particle  
implemented in the standard force fields. Gromacs also supports e.g.  
electron shells for polarization.

>
> 2) In ffG43a1.rtp, under the heading [atoms], what is the last number  
> after
> what appears to be the charge?

The charge group (must be contiguous). If you use long-range  
electrostatics like PME you could use a separate group for every atom,  
but it also speeds up neighborsearching slightly, so we always enable  
it by default.

>
> 3)  Finally, I have heard that Gromacs supports exponential type van  
> der
> waals potentials, but I don't see how to enable or disable this.  Or  
> how to
> use Lennard-Jones instead, etc.

That should be Buckingham potentials. Check the manual for instructions  
on how to specify the parameters in the force field files; the major  
force fields in the distribution all use Lennard-Jones interactions.  
Since densities are very sensitive to the exact parameters I don't  
think you'll get very accurate results by just fitting a Buckingham  
potential to the LJ parameters - use it if you already have Buckingham  
parameters or want to reparameterize.

A word of warning - The exponential function necessary is rather  
computationally expensive, so LJ is significantly faster. I couldn't  
implement it in SSE assembly for x86 either, since SSE lacks the exp()  
instruction.

Cheers,

Erik

> Any help would be appreciated.
>
> David Kendall
>
>
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Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
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