Hello!
1. It seems I have encountered a minor bug (?) in repl_ex.c for
version 4.6.x (for NPT simulations only):
Line 880 (in version 4.6.5):
fprintf(fplog, dpV = %10.3e d = %10.3e\nb, dpV, delta + dpV);
should be:
fprintf(fplog, dpV = %10.3e d = %10.3e\n, dpV,
OK, but with Berendsen you're also not observing physics. Your call.
Mark
On Wed, May 14, 2014 at 3:50 AM, Steven Neumann s.neuman...@gmail.comwrote:
Thanks a lot! Berendsen barostat works well with V-rescale using REMD, no
crashes observed.
On Tue, May 13, 2014 at 2:08 PM, Mark Abraham
On May 13, 2014 7:21 AM, Steven Neumann s.neuman...@gmail.com wrote:
Thanks a lot! So which combination of thermostat/barostat would provide a
proper ensemble without crashes?
Various - but only P-R for the barostat in GROMACS, so you must be
conservative with REMD exchange period. That will
Dear Gmx Users,
I am running REMD of a small protein in water. I have 36 temperatures.
After minimization I equilibrate each with nvt and npt ensemble. Then I
start REMD with -multidir. The mdp:
; Run parameters
integrator = md; leap-frog integrator
nsteps = 5000
dt =
What would you recommend then? Equilibrate with Berendsen barostat and
v-rescale thermostat?
On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/12/14, 3:58 AM, Steven Neumann wrote:
Dear Gmx Users,
I am running REMD of a small protein in water. I have 36
I would generally encourage the use of NVT REMD. However, note that P-R
does exhibit unstable oscillatory behaviour when not close to equilibrium.
REMD is supposed to stay in equilibrium by design, but this gets double
crossed if the exchange period is too short with respect to the
autocorrelation
Thanks a lot! So which combination of thermostat/barostat would provide a
proper ensemble without crashes? I am looking in the literature but did not
find anything.
On Tue, May 13, 2014 at 6:34 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
I would generally encourage the use of NVT REMD.
,
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of aperez
a.pervi...@gmail.com
Sent: 22 April 2014 12:46
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD, demux after 100 ns
.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher
Neale chris.ne...@alum.utoronto.ca
Sent: 02 May 2014 14:28
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD, demux after 100 ns per replica
Dear
Hi,
I did an extra modification to the *.pl with the aim of being more general
with the time step.
I have just added a line that asks the time step.
Note: I don't know perl, so I apologize for the rustic way how I modified
the file.
Thanks,
Andrea
proof_demux.pl
Hi all,
Today I have experienced a problem with the demux script applied in a
replica exchange simulation.
I have 16 replicas, and for each replica I have about 120 ns of MD.
When I executed the script demux.pl on the log file, I noticed that the
first column of the replica_*.xvg files had a
Hi,
Yes, I have seen this. Unfortunately that script dates from the days when
10ns was a long run, and like most things in GROMACS, hasn't seen much love
since one of the developers was actively using it. If you can test your
fixed version and want to contribute it back, you can follow the
expand upon the bug report.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of aperez
a.pervi...@gmail.com
Sent: 16 April 2014 11:48
To: gmx-us...@gromacs.org
Subject: [gmx-users
On 3/4/14, 11:26 PM, atanu das wrote:
Thanks Justin. That's reassuring. However, I was wondering if any smoothing
function is used in getting the melted fractions at intermediate temperatures
with 1-K resolution. I could not find it in the description of the g_kinetics
program. I need to know
Dear Sir,
I successfully ran demix.pl and generated the xvg files -
replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as
melt.xvg below ..
# This file was created Wed Feb 26 10:10:27 2014
# by the following command:
# g_kinetics_d -f replica_temp.xvg -d
On 3/4/14, 12:22 PM, atanu das wrote:
Dear Sir,
I successfully ran demix.pl and generated the xvg files -
replica_ndx.xvg and replica_temp.xvg. I am attaching the file that I got as
melt.xvg below ..
# This file was created Wed Feb 26 10:10:27 2014
# by the following
On 2014-03-04 00:20, atanu_das wrote:
Dear Gromacs users,
I have performed a REMD simulation with 12 replicas
exponentially spaced between 260-420K. However, when I applied g_kinetics
program to generate the melting curve, I got 161 values starting from 260K
to 420K having the
of Mark
Abraham mark.j.abra...@gmail.com
Sent: 24 February 2014 21:26
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] REMD slow's down drastically
On Feb 24, 2014 11:01 PM, Christopher Neale
chris.ne...@alum.utoronto.ca
wrote:
Presuming that you have indeed set up
sorry, and what performance did you expect from REMD?
Dr. Vitaly V. Chaban
On Mon, Feb 24, 2014 at 8:32 AM, Singam Karthick sikar...@yahoo.in wrote:
Dear members,
I am trying to run REMD simulation for poly Alanine (12 residue) system. I
used remd generator to get the range of temperature
Dear Francis
we are running in the Xeon E5-2670 8C 2.60GHz (2 CPUs , 8 cores, 16 threads)
for each temperature. and the exchange attempt frequency is 500 steps. The
other system with 126 replicas run 30 ns per day ( system size of ~38000
atoms). could you please help us in solving this
Adding replicas cannot of itself slow things down, though it will increase
the cost linearly. Don't try to run them all on the same amount of hardware
as a smaller calculation! You are shooting yourself in the foot if you do
not have at least one processor per replica (= MPI rank).
Mark
On Mon,
So what's the difference between the two systems? I think you can look
through the end of the log file, and find which part slowed down. Maybe
your job did not use the right partition of cores (too much comm. time)? I
don't know.
Francis
On 25 Feb, 2014 1:19 am, Singam Karthick sikar...@yahoo.in
.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Singam
Karthick sikar...@yahoo.in
Sent: 24 February 2014 02:32
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] REMD slow's down drastically
Dear members,
I
.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham
mark.j.abra...@gmail.com
Sent: 24 February 2014 21:26
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] REMD slow's
Dear members,
I am trying to run REMD simulation for poly Alanine (12 residue) system. I used
remd generator to get the range of temperature with the exchange probability of
0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its
drastically slow down the simulation time (for
Because every replica has to be calculated separately, it seems the speed
is not that slow (125 * 0.07 ~ 9 ns).
Also, to evaluate it, you should post how many CPUs you used, and other
information like exchange attempt frequency...
Francis
On Mon, Feb 24, 2014 at 3:32 PM, Singam Karthick
Sir,
I want to do an REMD simulation having 16 replicas. But I have only
8 processors. Is it possible to do 16 replicas in 8 processors? How I can
do this?
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Dear Gromacs users!
I'd like to perform replica exchange simulation
For this I've made bash script which create n folders like
replica-298
replica-312
replica-323
replica-334
...
replica-N
with all files needed for simulation considted of specified mdp file with
different ref_t value
No I'd
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight jmsstarli...@gmail.comwrote:
Dear Gromacs users!
I'd like to perform replica exchange simulation
For this I've made bash script which create n folders like
replica-298
replica-312
replica-323
replica-334
...
replica-N
with all files
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