Regarding amber parameters using NAMD

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon May 04 2009 - 03:22:27 CDT

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?

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?

Any help - appreciated thanks in advance

Best
J

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