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
