Re: NAMD Simulation in a laptop

From: Denish Poudyal (qrystal45_at_gmail.com)
Date: Sun Mar 25 2018 - 21:37:28 CDT

On Mon, Mar 26, 2018 at 7:52 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>

Water is used as solvent explicitly with NaCl of 0.15 mol/l used to ionize
the system. And the simulation is done at 2 fs/step with spherical boundary
conditions. CHARMM Force fields are being used. As I'm very much new to
this method, please suggest how can I conduct this work smoothly.

-- 
*Denish PoudyalCDPTU, Nepal*

This archive was generated by hypermail 2.1.6 : Wed Dec 11 2019 - 23:19:45 CST