Re: Using restraint on the dye using radius of gyration value in namd

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 02 2018 - 10:40:18 CDT

http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_gyration
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic

On Mon, Apr 2, 2018 at 10:26 AM, Life Sciences Inc <
contact.lifesciences.inc_at_gmail.com> wrote:

> Hi All
>
> I want to put restraints on the "cluster of the dye" embedded inside the
> lipid bilayer according to the clustered dye radius of gyration value,
> which I already have the total value of the radius of gyration at the
> certain time frame. I want to place that particular value of the radius of
> gyration using NAMD on the headgroups of the dye to start the simulation so
> that my dye remains in clustered form throughout the simulation run can
> anyone please tell me what would be the input file for the colvar related
> to restraints according to the radius of gyration value?
>
> Thank you
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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