Hi,
Hi Andrea,
I think it's a good thing to start another simulation by mutating the
[EMAIL PROTECTED] Besides, it would be good to mutate the [EMAIL PROTECTED]
back, to
see if it goes the other way. In any case, you'll have to perform
multiple simulations. For a strategy on comparing
Hi Chris,
the patch can be downloaded from the gromacs website:
download - user contributions - contributed software - gmx_alltoall
Carsten
[EMAIL PROTECTED] wrote:
This is a fantastic development. I had wondered why my scaling was so
much better for openmpi than for lam. Has the patch been
Thanks for the reply. Are you sure that it is there? I checked that
prior to sending the fist request and I checked it again now. Ordered by
date, the most recent entry is StressCPU, version 2.0 09.02.2007 and
next is g_spatial 21.12.2006. In any event, I cleared my cache, used
the reload
On Tue, Apr 03, 2007 at 10:16:12AM -0400, Chris Neale wrote:
Thanks for the reply. Are you sure that it is there? I checked that
prior to sending the fist request and I checked it again now. Ordered by
date, the most recent entry is StressCPU, version 2.0 09.02.2007 and
next is g_spatial
David van der Spoel wrote:
Steve Fiedler wrote:
Thank you for looking over the input and for suggestions Mark.
Unfortunately, a comparison of the topologies with diff revealed no
inconsistencies. GROMACS can correctly recognize the presence of the
significant repulsion (e+10) between atoms
I have found it. Thanks for your patience, I don't know how I missed it.
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Please search the archive at http://www.gromacs.org/search before posting!
I have a question about simulating metal ions in aqueous
solution at an infinite diluition: say I have a metal ion
(such as Ca2+ or Mg2+) and about a thousand water molecules.
I have to compensate the non zero charge of the system
with negative ions?
As I can understand the use of a reaction
Hi Gleb,
Apparently I wasn't clear enough. g_rmsdist calculates the average
distance for each pair of atoms over time and then calculates, for
each frame, the deviations from the average distance for each pair of
atoms. Per frame, these deviations are summed and the square root is
taken.
You're
Hi
I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like to
try
the GROMACS patch for better all-to-all, as well as the all-to-all test
program referred
to on the paper. I can't find it on the GROMACS site.
We've got a Cisco 6500 and when I run tcpdump during MPI runs I see a
Howdy,
We are bringing a one rack (1024 node) IBM Blue Gene/L system online.
I've been tasked with compiling Gromacs for the Blue Gene. We have the
XL compilers installed (blrts_xlc / mpixlc, etc), so I'll be using those
rather than GNU.
Has anyone on here successfully cross compiled
All,
I'm using the CVS version of 3.3.1 from last week, and am trying to
get the new pairs types Berk Hess has implemented to work for doing
decoupling. There's an old e-mail here on the subject, which is all
I've got to go by:
Have a digg in the mailing list. I remember that someone has once shared...
On 4/4/2007 6:15 AM, Mike Hanby wrote:
Howdy,
We are bringing a one rack (1024 node) IBM Blue Gene/L system online.
I've been tasked with compiling Gromacs for the Blue Gene. We have the
XL compilers installed
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