Re: equilibrating the system with constrained Protein

From: Peter Freddolino (
Date: Thu Sep 14 2006 - 13:40:37 CDT

Hi Dhiraj,
please have a look at the NAMD manual entry on constraints
(, and the
gramicidin tutorial
( and
subsequent pages). In brief, you need to make a separate pdb file that
has the atomic coordinates you want to constrain things to, and
containing a spring constant in either the beta or occupancy field.

Dhiraj Srivastava wrote:
> Hi All
> I have solvated my protein in water and now trying to equilibrate it
> with protein molecule constrained for not to move. How can i do that. can i
> set B 1 but then when i will start normal Molecular Dynamics Simulation
> then
> how will i change the B to its normal old value.

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