hi gmx-users,
i haven't been able to accomplish the following:
i have a system with n atoms, and i want to remove the degrees of freedom
for some of the atoms during different moments of the simulation
for example, assume the primary sequence of my protein is a-b-c-d-e-f-g,
and, for the first 50 picoseconds, i know that b, c and d move as a
"group", and so i want to remove the degrees of freedome between b and c
and between c and d, and have {bcd} move as one unit; then, at time 50-100
picoseconds, atoms b, c and d no longer more as a group, but atoms d, e, f
and g move as a group, so for the integration step from 50 to 100
picoseoncds, i would want to remove the degrees of freedome between d and
e, between e and f, and between f and g
this is similar to fixing all but the active site of a protein and only
performing md on only the active site, but not quite the same
any suggestions?
thanks much!
filip
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