Re: NAMD Simulation in a laptop

From: Denish Poudyal (qrystal45_at_gmail.com)
Date: Sun Mar 25 2018 - 23:34:38 CDT

I really appreciate your suggestion as I didnt have that idea until this
and obviously there are no such centers nearby me, I'll try finding one.
Thank you.

On Mon, Mar 26, 2018 at 10:11 AM, Richard Overstreet <roverst_at_g.clemson.edu>
wrote:

> Denish,
>
> I would submit a proposal to a supercomputer center for an allocation of
> CPU/GPU walltime. In some cases an initial allocation is fairly easy to
> get. Laptops aren't really suited to running heavy computational jobs. As
> axel said there is always a choice.
>
> Regards,
>
> Richard
>
> On 03/25/2018 10:37 PM, Denish Poudyal wrote:
>
>
>
> 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 Poudyal CDPTU, Nepal *
>
>
>

-- 
*Denish PoudyalCDPTU, Nepal*

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