Re: simultaneous simulation for protein in water and SMD

From: Axel Kohlmeyer (
Date: Thu Oct 03 2013 - 07:39:03 CDT

On Thu, Oct 3, 2013 at 2:33 PM, amit banerjee
<> wrote:
> Dear Friends,
> I have a query regarding running simulation of a protein
> in water and performing SMD concurrently.
> Although, i was able to run individual simulation, first protein in water
> sphere/water box followed by SMD.
> Both the simulation was tested in quad core linux and windows system
> successfully. For 1ns simulation it took long time for each case.
> I would like to know in a quad core single system (linux/windows) is it
> possible concurrently running both the simulations, i.e., protein in water
> and SMD, by altering the configuration file.
> My objective is to shorten the time period for overall simulations.

you cannot cheat physics. well, not unless you are a rare genius. what
use is to have results faster, if they are incorrect?

so the only way to get your work done correctly and faster is to get
hold of more CPUs. NAMD parallelizes very well and there are plenty of
parallel compute resources. it only takes some effort to get hold of


> Any helpful suggestion will be appreciated, suggestions with some .conf file
> in this regard will be additionally helpful for me.
> looking forward for your suggestions.
> Amit K. Banerjee
> Indian Institute of Chemical Technology,
> India.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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