Re: impose restraint on the internal coordinate of protein

From: Giacomo Fiorin (
Date: Mon Jun 21 2010 - 16:09:20 CDT

Hi, my suggestion is to try out the collective variables module in NAMD
2.7b1 and 2.7b2 (as usual, use the more recent version when in doubt). You
can set up two variables of RMSD type, and apply them a soft boundary
potential that begins at zero, or slightly above. Since you have two
separate chains for each dimer, keep into account the effects on wrapping:
there is a note about this in the collective variables section of the NAMD


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 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
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On Mon, Jun 21, 2010 at 2:43 PM, dhacademic <> wrote:

> Hi, I have a question about imposing restraint on protein.
> In my system, a dimer-of-dimer structure (protein) is merged in a water
> box, say dimer A (with monomer a and b) and dimer A' (with monomer a' and
> b'). I want to keep the structures as well as the relative orientation
> within the dimer, but to search the optimal orientation between the two
> dimers by MD simulations. How can I impose this kind of restraint in NAMD?
> Thanks in advance.
> Hao Dong

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