[gmx-users] Replica exchange simulations more than number of processor

[Christopher Neale]

Just my 2 cents: REST2 doesn't work. The random walk is much better than REST but the sampling efficiency at low lambda is now poor. Your mileage may vary, but be aware that REST2 is not necessarily going to be useful for all systems.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Thomas Piggot <t.piggot at soton.ac.uk>
Sent: 14 April 2017 09:23:35
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Replica exchange simulations more than number of processor

In addition, using another technique like REST2 may substantially reduce
the numbers of replica's you need. Still, more compute is definitely
recommended if you can get it.

Cheers

Tom

On 14/04/17 12:48, Smith, Micholas D. wrote:
> You can try over assignment of cores, but that will be horribly slow. Or use more than 1 node (if you can get it).
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Мижээ Батсайхан <b.mijiddorj at gmail.com>
> Sent: Friday, April 14, 2017 4:16 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Replica exchange simulations more than number of   processor
>
> Dear gmx users,
>
> I would like to simulate folding of a peptides. I have only 12 core
> processor, and I assumed the number of replica using temperature generator
> as following link
> http://folding.bmc.uu.se/remd/.
>
> The number of replica is about 60. How can I solve this problem? Can you
> advice me, please?
>
> Best regards,
> Mijee
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--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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