[gmx-users] Question about the pairs parameters

Yanmei Song ysong30 at asu.edu
Thu Jan 29 19:04:01 CET 2009


If I want to define non bonded interactions in my top. I already have
the sigma and epsi values. What I wanted to do is to to use
combination rule 2, then how should I write the pairs part?

ai  aj  fu    c0, c1, ...
   1   6   1                                           ;   CAA  CBH
   2   7   1                                           ;   CBF  CAG
   2   8   1                                           ;   CBF  CAH
   2   9   1                                           ;   CBF  OAY
   3   6   1                                           ;   CAB  CBH
   4   6   1                                           ;   CAC  CBH
   5  10   1                                           ;   OAW  CBJ

So does the function here means the combination rule, or I need to
define it in [defaults] ? if it is the latter, then what does the
functions means here? The value i need to put here for c0 and c1 then
should be sigma and epsi, right?  Thank you so much for your answer in
Yanmei Song
Department of Chemical Engineering

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