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: Fri Jul 29 2011 - 12:40:27 CDT

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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

• Next message: David Brandon: "'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany"
• Previous message: Ajasja Ljubetič: "Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds)"
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