Re: Steered Molecular Dynamics

From: Mert Gür (
Date: Wed Aug 05 2009 - 06:57:17 CDT

Dear Gaurav,
I think it depends on wheter your system deviates from this vector direction
during pulling. In other words the unit direction vector between your fixed
atoms and SMD atoms should be approximately the same durring simulation.
I hope this will be of any help.

On Fri, Jul 31, 2009 at 8:33 AM, gaurav bhatti <>wrote:

> Hi
> I posted my question in some other thread earlies. I am sorry for the
> mistake.
> I want to use steered molecular dynamics to pull two domains of a protein
> apart from each other. I plan to do in by constraining domain 1 and applying
> a constant velocity to the domain 2. I know that I can constrain domain 1 by
> setting the B or Occupancy column of these atoms as 1 and using that as
> reference for constraints. Also I think I can select the SMD atoms in the
> same way. My problem is with the direction of pulling. I can calculate the
> center of masses of the two domains and then apply velocity along the
> direction : COM2 - COM1. Is this a good strategy?
> Gaurav Bhatti
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