VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Sep 15 2014 - 19:41:49 CDT

Hi Natnael,

I'd use the colvars module of NAMD, or the colvars module in concert
with standard constraints and restraints, depending on what your
constraints look like. This would be the pseudocode if you took the pure
collective variables approach:

colvar {
name high
..
}
colvar {
name low
..
}
harmonic {
name permanent
colvars high
..
}
harmonic {
name relaxed
colvars low
forceConstant 1.0
targetForceConstant 0.0
..
}

Where "..." stands in for alot of things you can fill in depending on
your system based on the appropriate details in the NAMD user guide.
Just as a warning, this is very much a namd-l kind of question, rather
than a vmd-l one.
-Josh Vermaas

On 09/15/2014 06:21 PM, Natnael Doilicho wrote:
> Hi all,
>
> I would like to set a high constraint on one set of atoms with a
> constant constraint coefficient throughout my simulation while at the
> same time setting a low constraint on a separate set of atoms (a
> protein backbone) and relaxing that constraint coefficient gradually
> to release the protein.
>
> How can I set these two separate constraints?
>
> Thanks,
> Natnael Doilicho
> University of Chicago
>