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

[Szilárd Páll]

On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> 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.


Interesting. Is there any (published) data you could point to that supports
this?


> 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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