Re: How to restraint pairinteractions

From: Family Xu (
Date: Thu May 31 2012 - 11:29:11 CDT

Hi Giacomo, Sorry for the confusion. The pairinteraction which I want to be
the reaction coordinate of PMF is the interaction energy between two group
atoms (for example, the interaction energy between two residues). Hope this
is clear now.


On Wed, May 30, 2012 at 5:15 PM, Giacomo Fiorin <>wrote:

> Hello Sanxing, can you please write in more detail what do you mean by
> "pairinteractions"? It may very well be that you can do this easily, both
> with colvars and with tclForces.
> On Wed, May 30, 2012 at 6:01 PM, <> wrote:
>> Dear NAMD users,
>> I am trying to run NAMD simulation to generate the PMF with
>> pairinteractions as a reaction coordinate.
>> One way to do this is to use the colvar module in NAMD, umbrella sampling
>> followed by WHAM. Unfortunately, in terms of the user guild of NAMD,
>> pairinteraction is not the predefined colvar in NAMD.
>> Therefore, I am wander if this can be done by using the user defined
>> force (tclforce). But I don't know how. Could you please let me know
>> whether you have any suggestions to solve this issue?
>> Thanks.
>> Sanxing

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