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 simu
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 ty
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 so
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What I have is only my own personal unpublished data.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
I too also fairly frequently use the -maxwarn option for this message.
Perhaps it would be better off as a grompp note rather than a warning,
or am I missing something here? This way, there isn't an encouragement
for people to use the -maxwarn option for other situations when it is
less appropr
Dear users,
Can you please inform me, which LINCS condition (h-bond, all bonds etc.)
should be used during final production run to get the most realistic
results?
Thanks & regards,
Saumyak
--
*Saumyak Mukherjee*
Junior Research Fellow
Prof. Biman Bagchi's Group
Yup, I use maxwarn all the time in that case. It's safe for general usage.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Anurag Dobhal
Sent: 14 April 2017 12:43:18
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users]
Dear Gromacs usrs,
I am running a umbrella sampling simulation between two identical polymer
chains in water using OPLS AA force field. My system does not have any
charge. I have successfull generated the different configurations.
While running the "gmx grompp -f npt_umbrella.mdp -c conf0.gro -p
What I have is only my own personal unpublished data.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 no
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 su
Is this on your personal laptop or on a cluster? On a cluster, perhaps you have
hit your user or group quota for file size or number of files (especially if
you are running in $HOME or something). I have also seen this when there really
should be space available, but the issue was (again on a la
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
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
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
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, plea
15 matches
Mail list logo
