[gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

Justin A. Lemkul jalemkul at vt.edu
Sat May 5 15:46:30 CEST 2012

On 5/5/12 9:39 AM, Marcelo Lopez wrote:
> Hi, all, I'm still confused about how to set up 1-4 interaction tables
> for tabulated non-bonding potentials when using the -tablep option in
> mdrun.
> The specific question is:
> How must I specify the 1-4 interaction in those tables? How many
> columns and with what?
> My primary goal is to set all the 1-4 interactions equal to zero. I
> have some 1-4 pairs that aren't involved in dihedrals, that means that
> setting up
> nrexcl = 3
> and
> gen-pairs = no
> isn't enough
> Please, someone help me to understand. If you don't have the time,
> just copy/paste a table.
> Thank you very much.

I'm not sure you even need tables.  Wouldn't the following do what you want?

[ pairs ]
x  y   1   0.0  0.0

Explicitly setting zeroes for C6 and C12 should override anything in [pairtypes] 
for a given pair of atoms (replacing x and y with actual numbers), I believe.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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