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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas Piggot
<t.pig...@soton.ac.uk>
Sent: 14 April 2017 14:16:26
To: gmx-us...@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What I have is only my own personal unpublished data.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-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Szilárd Páll
<pall.szil...@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.ne...@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-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas
Piggot <t.pig...@soton.ac.uk>
Sent: 14 April 2017 09:23:35
To: gmx-us...@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-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Мижээ
Батсайхан <b.mijidd...@gmail.com>
Sent: Friday, April 14, 2017 4:16 AM
To: gromacs.org_gmx-users@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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