Dear Amber users/developers,
I apologize, as it is a duplicate message. The following issue is very
important for me.
I ‘m trying to do some steered MD simulations with pmemd 12 in which the
distance between two atoms must be increased while the angle made between
three atoms must be fixed at its initial value. I know that this kind of
simulations is performable easily by using jar and ncsu_pmd in sander.
However, it seems that ncsu code is not accessible in pmemd. On the other
hand, if two restraints are added in the restraint file for steered MD (one
for increasing the distance and another for keeping the angle constant),
only the first restraint in the restraint file would be applied and the
other would be ignored by the code. Is there a way to perform this kind of
simulations through pmemd 12? I'd be so grateful if anyone could help me on
these issues.
Kind regards,
AMNN
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Received on Thu Sep 20 2012 - 10:00:03 PDT
