Re: NAMD/metadynamics

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Fri Mar 26 2010 - 09:14:17 CDT

Hello Neville, why did you send the message twice?

Metadynamics is implemented in NAMD 2.7b2, correct. The convergence
of the method depends entirely on the properties of the system and on
the choice of your variables.

Regarding multiple walkers, there was a message exactly two weeks ago
on this mailing list. The subject will be most likely part of a
metadynamics tutorial.

Giacomo

---- ----
 Giacomo Fiorin
   ICMS - Institute for Computational Molecular Science
     Temple University
     1900 N 12 th Street, Philadelphia, PA 19122
 work phone: (+1)-215-204-4216
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---- ----

On Thu, Mar 25, 2010 at 10:16 PM, neville forlemu
<neville_forlemu_at_yahoo.com> wrote:
> Hello,
> I understand NAMD2.7b2 has the metadynamics patch included. I was wondering
> whether somebody who has used it before can comment on how well it speeds up
> convergence of rare events, and secondly whether one can use a multiple
> walker strategy with this metadynamics colvar module as is implemented in
> the NAMD/PLUMED compilation.
>
> Thanks
> Neville
>
> ________________________________
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: Priyan Amaras <priyan.amaras_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Wed, March 24, 2010 11:41:50 PM
> Subject: Re: namd-l: NAMD with two GPUs
>
> perhaps your system is not large enough?
> i assume you do use two processors.
>
> a.
>
> On Wed, Mar 24, 2010 at 10:35 PM, Priyan Amaras <priyan.amaras_at_yahoo.com>
> wrote:
>> Hi Everyone,
>> I running simulations with two GPUs. I use this command to run the
>> simulation.
>>
>>  ./charmrun ++local +p<procs> ./namd2 +idlepoll +devices 0,1 <configfile>
>>
>> But the simulation speed with two GPUs is no different from the speed with
>> only one GPU.
>>
>> Do I have to do anything else in order to utilize the second GPU?
>>
>> Thanks,
>> Priyan
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
>

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