Re: Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed

From: Ehsan Ban (ehsan.ban_at_gmail.com)
Date: Mon Aug 15 2011 - 00:01:22 CDT

Thank you very much Yi.

That was helpful. Further, I think in my case using Tcl Boundary Forces can
give me more control over the process:

http://www.ks.uiuc.edu/Research/namd/2.8/ug/node51.html

Parts of the tutorial Stretching Deca-Alanine can be a big help for that:

http://www.ks.uiuc.edu/Training/Tutorials/#deca

Bests,
Ehsan

2011/7/29 Wang Yi <dexterwy_at_gmail.com>

> You can use ColVar. Maybe just set the target timestep to be 1.
>
>
> http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node49.html#SECTION000123700000000000000
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> 2011-7-291:40 Ehsan Ban д
>
> Hi,
>
> I want to stretch a molecule by holding one C atom fixed in position and
> moving another C atom. I've been moving the C atom with SMD, which moves
> with a constant velocity and affects its position in every timestep. Now I
> want to do something similar but with a little difference.
>
> I want to displace the atom 1A0 in one timestep and then holding it fixed,
> run MD for 10,000 timesteps and just relax the system in that state and then
> displace one more 1A0 step and relax again. I'm looking for a solution
> applicable to running parallel runs on a blue gene machine with SLURM job
> management system.
>
> I appreciate your help.
>
> Thank you
> Ehsan
>
>
>

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