From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Sep 11 2010 - 04:02:52 CDT
Hi Hao,
> I have carefully read the harmonic restraints part in NAMD 2.7b3 manual. My
> understanding is as follow: If I want to implement TMD calculations with
> colvars, the following 4 keywords are necessary in the harmonic restraint
> part of colvars config file, while the rest keywords are just optional:
>
> (1) "centers", the initial value of the center of the restraint potential.
> (2) "targetCenters", the final value of the center of the restraint
> potential.
> (3) "targetNumsteps", the total steps that RMSD changing from the initial
> value to the final value under the restraint potential.
> (4) "Force constant", the force constant imposed on the restraint potential.
>
> Am I right?
That's right, adding of course the "colvars" option to specify which
colvars this restraint applies to. Also, this is for a moving
restraint (such as TMD). For a fixed restraint, you would just need
"colvars", "centers" and "forceConstant".
Best,
Jerome
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