On 19/03/2012 9:06 PM, Asaf Farhi wrote:
Dear Gromacs user
Hi. My name is Asaf and I'm trying to edit potential parameters for
the non bonded interaction potential terms between specific atoms (k1
for 1 subset of pairs and k2 for anoother subset of pairs).
Is the pairs section in the topology file the correct place to do
this? and if so how would you incorporate spring constant for
particular pair interaction?
Check out the options described in chapter 4 of the manual. You need to
know whether you want a force that varies with some power of 1/r (change
nonbonded interaction) or with r (various other possibilities with
various side effects, bells and whistles).
Mark
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