, 2010 5:13
Subject: RE: [gmx-users] Replica Exchange MD on more than 64 processors
To: Discussion list for GROMACS users gmx-users@gromacs.org
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Hi,
One issue could be MPI memory usage.
I have noticed that many MPI
Dear list
I recently came up with a problem concerning a replica exchange simulation. The
simulation is run
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,
intel compiler version 11.0
mvapich version 1.1.0
mkl version
double precision,
which is almost never required. This will also make your simulations
a factor 1.4 faster.
Berk
Date: Tue, 2 Feb 2010 18:55:37 +0100
From: breue...@uni-koeln.de
To: gmx-users@gromacs.org
Subject: [gmx-users] Replica Exchange MD on more than 64 processors
Dear list
I
Dear list
I recently came up with a problem concerning a replica exchange simulation. The simulation is run
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,
intel compiler version 11.0
mvapich version 1.1.0
mkl
On Mon, 28 Dec 2009, David van der Spoel wrote:
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar
bharat v. adkar wrote:
On Mon, 28 Dec 2009, David van der Spoel wrote:
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures.
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a
'protein in
water' system. I am following instructions
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a
bharat v. adkar wrote:
On Mon, 28 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
On Sun, 27 Dec 2009, Mark Abraham wrote:
bharat v. adkar wrote:
Dear all,
I am trying to perform replica
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures. As per advise on wiki, I equilibrated the system at
respective
bharat v. adkar wrote:
Dear all,
I am trying to perform replica exchange MD (REMD) on a 'protein in
water' system. I am following instructions given on wiki (How-Tos -
REMD). I have to perform the REMD simulation with 35 different
temperatures. As per advise on wiki, I equilibrated the
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