Ok, the redmine is filled up and anybody who has time to help finding the issue
is welcome :) I can't do much more!
As an alternative a colleague suggested that I could potentially get around the
problem by using a compilation combining Open-MP or thread-MPI for each replica
running on one
I finally could reproduce the problem in gmx461 and have fled up a red mine
report.
I hope we can fix this easily but I am not sure how things go go from now!
Someone will get the bug assigned and fix it when ever possible or something
else?
Thank you all for the help,
XAvier.
On May 2,
mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Thursday, 2 May 2013, 11:53
Subject: Re: [gmx-users] issue in replica exchange
On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote:
Ok here is my current status on that REMD issue
Summarizing!
On Fri, May 3, 2013 at 12:31 AM, XAvier Periole x.peri...@rug.nl wrote:
Are confirming that you reproduce the problem with gmx-4.6.1 or simply
summarizing in case we lose track :))
On May 2, 2013, at 23:31, Michael Shirts mrshi...@gmail.com wrote:
So to summarize -- the
On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote:
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
I'm running remd in NPT ensemble for a small peptide and all is ok if the
maximum temperature is below 510/520 kelvin. I use Nosé-Hoover termostat
and Parrinello-Rahman barostat. Ref T from 285 to 500K and ref P equals to
1bar. Gromacs version 4.5.5. Exchange trials every 5 ps.
If I try to add
Did you look at some data like temperature/pressure/box size/Epot as a function
of time and especially around some exchanges?
Your system is atomistic I presume.
On May 2, 2013, at 12:38 PM, Simone Conti simone...@gmail.com wrote:
I'm running remd in NPT ensemble for a small peptide and all
I saw that redmine report, which could be related but it seems to happen only
for runs done outside the domain and particle decompositions.
I'll fill up a red mine.
Anything I could do to help speeding the fix?
On May 2, 2013, at 11:53 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On
Yes, my system is described at atomic level.
No, I can't see any strange value around exchanges. I analyzed only a
very little number of trajectories, but temperature, volume, potential
energy, pressure seem all to be around normal fluctuations.
2013/5/2 XAvier Periole x.peri...@rug.nl
Did
Could you send me a set of tar files that I could look at things the same way I
do with my system? I would guess that 6 tar files where you same energies and
print log file every step but xtc and trr files not that often would be really
cool.
You can send them directly to my email
I mean tpr files not tar! Autocorrection is sometimes funny :))
On May 2, 2013, at 2:11 PM, XAvier Periole x.peri...@rug.nl wrote:
Could you send me a set of tar files that I could look at things the same way
I do with my system? I would guess that 6 tar files where you same energies
and
On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote:
I saw that redmine report, which could be related but it seems to happen
only for runs done outside the domain and particle decompositions.
I'll fill up a red mine.
Anything I could do to help speeding the fix?
Quick check here -- is 4.6 behaving correctly? I actually spent some
time working on REMD in 4.6, and it seems to be behaving correctly in
my hands with temperature and pressure control.
Thanks for any additional info on this!
On Thu, May 2, 2013 at 8:18 AM, Mark Abraham
You mean working with or working on the code?
I'll try gmx-4.6.1
On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote:
Quick check here -- is 4.6 behaving correctly? I actually spent some
time working on REMD in 4.6, and it seems to be behaving correctly in
my hands with
Both. So if 4.6.1 doesn't work, I want to know so we can patch it
before 4.6.2 comes out. If it does work, then there is probably stuff
that can be backported.
On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote:
You mean working with or working on the code?
I'll try
Some good news …
The tpr files provided by Simone do NOT show abnormal behaviour! This good news
:))
However after turning ON the particle decomposition option to mdrun (-pd) I got
a warnings of water not being able to be settled and a crash. This was still
with Simone's trips … I took
I'll look at the 4.6.1 version next week, I could install it but I got a
conflict between the environmental variable defining openMP variable but I
turned it off during compilation …
You could try to run on particle decomposition to see if you get a problem … it
should one quite quick.
On
So to summarize -- the problem appears to be with particle decomposition.
On Thu, May 2, 2013 at 4:15 PM, XAvier Periole x.peri...@rug.nl wrote:
I'll look at the 4.6.1 version next week, I could install it but I got a
conflict between the environmental variable defining openMP variable but I
Are confirming that you reproduce the problem with gmx-4.6.1 or simply
summarizing in case we lose track :))
On May 2, 2013, at 23:31, Michael Shirts mrshi...@gmail.com wrote:
So to summarize -- the problem appears to be with particle decomposition.
On Thu, May 2, 2013 at 4:15 PM, XAvier
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
The symptoms: explosion of the system after 2-5 steps following the swap,
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the
ensemble data. The coupling to P and T and not exchanged with it?
The code in
Hi,
I have been recently using the REMD code in gmx-407 and gmx-453 and got a few
systems crashing for unclear reasons so far. The main tests I made are using
gmx407 but it is all reproducible with gmx453. The crashing was also reproduced
(not necessarily at the same time point) on several
Thanks for the good report. There have been some known issues about the
timing of coupling stages with respect to various intervals between GROMACS
events for some algorithms. There are a lot of fixed problems in 4.5.7 that
are not specific to REMD, but I have a few lingering doubts about whether
Thanks for the answer. I'll check gmx4.5.7 and report back.
I am not sure what you mean by GROMACS swaps the coordinates not the ensemble
data. The coupling to P and T and not exchanged with it? That would explain
what I see, but let see what 4.5.7 has to say first.
Tks.
On Apr 25, 2013,
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