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

Fri Apr 14 21:23:11 CEST 2017

Dear Thomas:

Thanks for the suggestion. I have a way foward, I'm just being selective about what I share at this point. This thread got a bit side-tracked from my reason for posting, which was simply to help a user with a single 12-core node to realize that dedicating it to a 6-month REST2 simulation might not be a good idea.
________________________________________
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 15:06:29
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Replica exchange simulations more than number of processor

Have you thought about a more selective scaling of the interactions
(i.e. HREX with only scalings applied for certain bits of the protein,
not the complete thing as in REST2) so as to reduce the protein
hydrophobicity at the lower lambda's? I've seen this selective scaling
work well in other types of system to counteract broadly similar types
of sampling issues at lower lambda's.

Just a thought, it might not work well for what you are doing,

Cheers

Tom

On 14/04/17 19:27, Christopher Neale wrote:
> In REST2, the protein becomes way too hydrophobic as lambda is decreased. Just run a standard simulation at 300K, another at 600K and then another one at 300K with REST2 lambda=0.5 and you'll see what I mean.
>
> REST has a hidden barrier corresponding to the point at which water becomes a theta solvent and the exchange is very poor across that boundary, with globular replicas staying at higher lambda and extended replicas staying at lower lambda. However, with REST2, there is no such hidden barrier because water never gets anywhere near being a theta solvent. So in REST2 you get good exchange for all the wrong reasons.
>
> Work continues....
>
>
> ________________________________________
> 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 14:16:26
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Replica exchange simulations more than number of processor
>
> Hi Chris,
>
> This is interesting. Do you have an idea why the sampling at low lambda
> values isn't very good?
>
> Cheers
>
> Tom
>
> On 14/04/17 17:40, Christopher Neale wrote:
>> What I have is only my own personal unpublished data. But add to that the number of years since REST2 came out and the low number of papers in which anybody did something useful with it and I'd say that suggests many others have tried and run into the same issues that I did (or maybe I'm just not reading the right papers, so please correct me if I am wrong). When my desired use failed I fell back to trp-cage folding in water and found the same things, so it's not like REST2 only fails for some exotic systems. Running 3 entirely separate repeats of regular T-REMD and 3 of REST2, I found that overall T-REMD is of similar or perhaps better efficiency (even though it has more replicas) compared to REST2. It's an on/off area of research for me, attempting to fix REST, but I still don't have a good answer for it.
>>
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Szilárd Páll <pall.szilard at gmail.com>
>> Sent: 14 April 2017 12:26:41
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Replica exchange simulations more than number of       processor
>>
>> 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
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>>> University of Southampton, UK.
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> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
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--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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