, 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
Hi,
One issue could be MPI memory usage.
I have noticed that many MPI implementations use an amount of memory
per process that is quadratic (!) in the number of processes involved.
This can quickly get out of hand. But 28 GB is a lot of memory.
One thing that might help slightly is to not use
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
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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