Re: NAMD Simulation in a laptop

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Mar 25 2018 - 21:07:13 CDT

On Sun, Mar 25, 2018 at 9:56 PM, Denish Poudyal <qrystal45_at_gmail.com> wrote:
> i thought I could run a 100 ns NAMD simulation in my laptop for a
> protein-hormone system containing around 2000 atoms in its pdb
> file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand
> steps, it has taken almost 4700 minutes. is this normal or its low?

nobody can give meaningful advice on such vague information. you're
not saying whether you are using implicit or explicit solvent, what
force field, what MD settings, how you run NAMD, which binary and
version you are using and so on.

NAMD prints out some benchmark information during the run, which can
help to make an estimate.

> the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any
> suggestions to run it faster???And I still am aware that using laptop for
> such work isnt advisable but I dont have a choice.

there *always* is a choice.

axel.

>
> Denish Poudyal
> CDPTU, Nepal
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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