From: DAI, JIAN (jdai2_at_fsu.edu)
Date: Mon Dec 10 2012 - 16:15:45 CST
Dear NAMD fellows:
We are calculating the free energy landscape of a protein using two distance restraints that describe the distance between two domains of the protein.
The problem is: I noticed that the boundary values of the colvars have constantly exceeded the restraint values. Although the force constants that are put on these distances are small, i.e., 1 kcal/mol A^2, the distances should not exceed the upperboundary and lowerboundary too much, shouldn't they? In the simulation, for example, when the boundary is set at
lowerboundary 9.0 and upperboundary 10.0,
the actual value of the second colvar drops down to even 7.3, which I think is way too low.
The configuration and colvars definition files are attached. Should we expect to see that these distance values exceed the boundary values or a stronger force constants will solve this problem? However, I've seen in another work that also uses a force constant of 1 (Wereszczynski and McCammon, 2012, PNAS).
Thanks in advance.
Jian
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