Re: Regarding amber parameters using NAMD

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Mon May 04 2009 - 10:41:52 CDT

Hi Jorgen,

On May 4, 2009, at 1:22 AM, Jorgen Simonsen wrote:

> Hi all,
>
> I have a simulation where I would like to use amber parameters
> instead of charmm. I have looked in the tutorial and it seems that
> it is possible to run.
>
> 1. Is it possible to freeze atoms during either minimization or MD
> simulation and where to add the constraint - normally I would use
> the B-column in the pdb file but it seems that is not included in
> the amber or is it?
>

After you build your system in AmberTools and get the prmtop and
inpcrd (topology/ff and coordinates, respectively), I am pretty sure
you can load one of those two files into VMD (I did this recently, but
I forget which one I used, but I know one of them works). From there
you just go about building the fixed/restraint pdb files as you
normally would using the B-column. Just writepdb as usual and stick it
in the config file.

> 2. As I would like to run a NPT simulation is it possible to use
> the langevin pistion for both the temperature as well as the pressure?
>

You would want to use both the Langevin Piston for your barostat and
the Langevin dynamics for your thermostat. You cannot control both
temperature and pressure with the langevin piston alone, as far as I
can tell from reading the user's guide.

Josh

> Any help - appreciated thanks in advance
>
> Best
> J

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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