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On 19/03/2012 9:06 PM, Asaf Farhi wrote:
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Dear Gromacs user<br>
<br>
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).<br>
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?<br>
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<br>
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).<br>
<br>
Mark<br>
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