[gmx-users] how to define a pair

nahren manuel mailnahren at yahoo.com
Wed Sep 4 13:29:06 CEST 2019

I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF). 
#include "toppar/charmm36.itp"
  [ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 2 yes 1.0 1.0

I want to add a pair between list of two atoms, say 10-500 (CA atoms). Lets say the distance between them is 0.800 nm. So I define my pairs in the following way,

10     500    1     (4*2.5*0.800**6)    (4*2.5*0.800**12) ; where 2.5 is my epsilon. I get some error when I run the simulation (infinite force, exploding simulation). I suspect my definition of C6 and C12 is wrong. Any suggestions would be useful.

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