More dimensions = more complex communication pattern. See
http://pubs.acs.org/doi/abs/10.1021/ct700301q
Note that it's not *always* x-y decomposition first, mdrun will look
at the dimensions of your system too. One case where manually
switching to 3D decomposition can be beneficial is when there
Exactly. The penalty of large nstlist is large buffer (rlist), but up
to 40-50 with CPUs and up to 100 with GPUs is quite realistic.
Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in
the mdp. From 5.0 there will be a command line option.
Cheers,
--
Szilárd
On Thu, Feb 6, 2014
PS: The buffer is automatically calculated based on the
verlet-buffer-drift set in the mdp file, for more details see the
appendix of http://dx.doi.org/10.1016/j.cpc.2013.06.003.
--
Szilárd
On Thu, Feb 6, 2014 at 11:04 AM, Szilárd Páll pall.szil...@gmail.com wrote:
Exactly. The penalty of large
Note that your above (CPU) runs had a far from optimal PP-PME balanc
(pme mesh/force
should be close to one).
Performance instability can be caused by a busy network (how many
nodes are you running on?) or even incorrect affinity settings.
If you post a/some log files, we may be able to tell
Dear users,
I'm trying to do NMA of a structure. When I minimize a structure:
Polak-Ribiere Conjugate Gradients converged to Fmax 10 in 3742 steps
Potential Energy = -5.2965824e+04
Maximum force = 8.0245171e+00 on atom 3038
Norm of force = 1.3228445e+00
When I try to perform a
Preso appuntamento per sabato mattina...di al papa' che si tenga libero!!!
Ivan
On 02/06/2014 11:09 AM, Szilárd Páll wrote:
PS: The buffer is automatically calculated based on the
verlet-buffer-drift set in the mdp file, for more details see the
appendix of
On 2/6/14, 3:26 AM, Jernej Zidar wrote:
Hi,
I have a polymer system composed of three molecules (I generated it
by taking one molecule and 'copied' along the y axis). Now, I'trying
to compute the radius of gyration of one of these molecules. When I do
the analysis for the smallest system,
Hello.
I'm trying to make a dynamic selection in protein-water complex for further
analysis. It looks like there's no support for dynamic selections in the
GROMACS tools such as trjconv, g_sas and others. Is there some progress
with dynamic selections in the recently announced GROMACS 5?
--
Double precision result:
http://comments.gmane.org/gmane.science.biology.gromacs.user/62746
Ahmet Yıldırım
6 Şub 2014 tarihinde 15:39 saatinde, Justin Lemkul jalem...@vt.edu şunları
yazdı:
On 2/6/14, 8:25 AM, Ahmet yıldırım wrote:
Dear users,
I'm trying to do NMA of a structure. When
On 2/6/14, 9:27 AM, Gmail2 wrote:
Double precision result:
http://comments.gmane.org/gmane.science.biology.gromacs.user/62746
I assume you mean to say that you're having the same issue as described in that
thread? You'll note that Michael mentions the existence of a bug, which has
since
First of all, Justin is right. Without commands and exact selections we
can't help much.
Second: Why don't try using VMD for calculating RG? - I ask the opposite,
ie. why use VMD when you got a native tools to do such? It's like using
genuine Nespresso capsules on a white-label machine when you
Hi users,
I've searched the web for tools that convert atom names in pdb files from e.g.
gromos nomenclature to amber or stockholm lipid nomenclature, but with no luck.
Manually mapping the atom names is obviously error prone, so if anyone know of
a script or a smart approach for this, do
Hi,
Does anyone know if there is a way to incorporate a nitroxide spin labels
into a gromacs simulation of proteins in water. With NMR and EPR it is
possible to obtain distance restraints between labels, and I am interested
to incorporate these restraints into my simulation. If there is a way to
VMD is an alternative, it was my suggestion. I know my similar was similar
to ignoring the original questions.
Besides, he can calculate end to end distance if he wants. Anyway, you are
right:).
On Thu, Feb 6, 2014 at 4:32 AM, Ali Alizadeh
ali.alizadehmoja...@gmail.comwrote:
Dear Jernej,
On Mon, Mar 4, 2013 at 3:22 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi yunsh...@gmail.com wrote:
Hi all,
I have read http://www.gromacs.org/Documentation/Cut-off_schemes, but
still unsure about how Verlet works.
The group cut-off scheme
Hi Erik,
It's not a very smart approach, but I have a very basic script that can
convert CHARMM36 (and probably Slipids as I think they are named and
ordered the same) into some united-atom force fields (43A1-S3, Berger,
53A6L and CKP). I can dig it out and send it to you off list, if you are
Hi Tom,
Yes. that sounds like a good starting point. Please send.
Erik
On 6 Feb 2014, at 19:39, Thomas Piggot t.pig...@soton.ac.uk wrote:
Hi Erik,
It's not a very smart approach, but I have a very basic script that can
convert CHARMM36 (and probably Slipids as I think they are named and
On Feb 6, 2014 8:42 AM, yunshi11 . yunsh...@gmail.com wrote:
On Wed, Feb 5, 2014 at 9:43 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
What's the network? If it's some kind of switched Infiniband shared with
other user's jobs, then getting hit by the traffic does happen. You can
see
On Feb 6, 2014 4:41 PM, akk5r ak...@virginia.edu wrote:
Hi,
Does anyone know if there is a way to incorporate a nitroxide spin labels
into a gromacs simulation of proteins in water. With NMR and EPR it is
possible to obtain distance restraints between labels, and I am interested
to
I'm not sure if I'm replying correctly, but I just wanted to mention that I
would love to file a report to the redmine list, but I have not been
approved to do so. Is there another place I can report this problem?
Will
On Mon, Feb 3, 2014 at 2:35 PM,
Hi!
Following Joao's suggestion I went to check all the commands I used,
I realized it was a typo. Namely, I was tellgin g_gyrate to use the
wrong index file with the right trajectory.
Thanks to everyone for helping out.
Jernej
On Fri, Feb 7, 2014 at 4:54 AM,
Hi William,
If you want to file a bug report you can do that at redmine.gromacs.org.
It seems that you are already registered, maybe twice:
wrww http://redmine.gromacs.org/users/853/edit Will Welch
wwelch...@gmail.com mailto:wwelch...@gmail.com
02/03/2014 11:33 PM
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