From: M. Madhu (madhu7_at_hotmail.com)
Date: Fri Nov 30 2007 - 10:22:48 CST
Dear NAMD users,
I would like to do a RMSD constrained dynamics. Is there anyway to do this in NAMD?
I did a TMD simulation where I gave same values for TMDInitialRMSD and TMDFinalRMSD.
Is it equivalent to a fixed RMSD constrained simulation?
In the NAMD manal (TMD section), it says "Forces are applied only if RMS(t) is betwween
TMDInitialRMSD and RMS*(t); in other words, only if the current RMSD fails to keep pace
with the target value."
Since TMDInitialRMSD and RMS*(t) are supposed to be same in this case, does it mean
that no forces are applied to maintain the RMSD? In addition, how can I obtain the constrained
force/energy in TMD simulations.
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