[gmx-users] Using pull code to keep two monomers near each other

Michael Daily mdaily.work at gmail.com
Sat Mar 8 01:19:05 CET 2014


I am trying to use the pull code to keep two peptide monomers near each
other during a replica exchange simulation of (homo)dimerization.  I do not
want any bias if the COM distance between the two is less than some value
r_max, as in umbrella sampling, i.e.

E = 0  for r_ij <= r_max;
E = k*(r_ij - r_max) for r_ij > r_max

Can this be done with the pull code or some other function? Pull=constraint
appears to essentially fix the COM distance, which I do not want to do


Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)

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