Dear All,
We are stuck with an error in domain decomposition for graphene layer, which is
periodic in XY plain (periodic_molecules=yes). The system runs perfectly on one
node, but when we try to use more than 1 MPI process it crashes regardless of
what we do:
Using 2 MPI processes
Using 4
Hello everyone,
what is the correct setup for simulations with no PBC and no cuttoffs in
Gromacs 5.0.4?
In versions 4.5 and 4.6 i used
nstlist = 0
ns_type = simple
pbc = no
This no longer works, as I get the error:
Domain decomposition does not support simple neighbor searching, use grid
Thanks for your quick reply, so it a fact that I can bypass the missing bonds
force constant field in grompp by using these constraints?
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf
Hi,
On Thu, Jun 11, 2015 at 1:26 PM ashish bihani ashish.bih...@outlook.com
wrote:
I extracted [was instructed to extract] trajectory frames at every 10 ps
from a 10ns xtc file and energy minimized each of them. How do I cluster
them?
I tried to do ls *.gro | gmx cluster -f {.}.gro , did
Hi,
Yes, there is no need or use for a force constant if the bond is rigid
(though IIRC you'll need to give grompp a dummy number anyway)
Mark
On Thu, Jun 11, 2015 at 11:51 AM Sotirios Dionysios I. Papadatos
si.papada...@edu.cut.ac.cy wrote:
Thanks for your quick reply, so it a fact that I
From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 134, Issue 66
To: gromacs.org_gmx-users@maillist.sys.kth.se
Date: Thu, 11 Jun 2015 11:37:49 +0200
Send gromacs.org_gmx-users mailing list submissions to
Dear community,
I am trying to set parameters for a molecule that doesn't exist in gromacs
library.
I have found all the required data from the literature, apart from bond force
constant (Kb).
There seems to be a way to overcome this but using constraints on all the bonds
using the Settle
Ok!
I solved the problem.
Basically it is possible to write the name of two groups for energygroups
that is written in index file.
On Thu, Jun 11, 2015 at 10:28 AM, gozde ergin gozdeeer...@gmail.com wrote:
Hi all,
I am simulating the organic-water system by using umbrella sampling method.
I
Dear Gromacs Users,
We're finally buying some Intel E52650 servers + NVIDIA GTX980 cards.
However, there's some servers that come with only PCI-e 3.0 x8 slots and
others with x16 slots.
Do you think this is relevant for gromacs performance ? And if so, how much
relevant ?
Thanks in advance.
Hi,
What David said, plus check out
http://www.gromacs.org/Documentation/Terminology/Reproducibility
Mark
On Thu, Jun 11, 2015 at 7:59 AM David van der Spoel sp...@xray.bmc.uu.se
wrote:
On 11/06/15 03:59, 范聪 wrote:
Hello, everyone!
I've run two molecular dynamics using gromacs with
On 11.06.2015 13:08, David McGiven wrote:
We're finally buying some Intel E52650 servers + NVIDIA GTX980 cards.
However, there's some servers that come with only PCI-e 3.0 x8 slots and
others with x16 slots.
Do you think this is relevant for gromacs performance ? And if so, how much
relevant ?
Hi,
SETTLE is a constraint algorithm for water. LINCS and SHAKE are the
available general-purpose constraint implementations - see the manual
section headed constraint algorithms.
Mark
On Thu, Jun 11, 2015 at 10:39 AM Sotirios Dionysios I. Papadatos
si.papada...@edu.cut.ac.cy wrote:
Dear
On 11/06/15 11:53, Jan Jirsák wrote:
Hello everyone,
what is the correct setup for simulations with no PBC and no cuttoffs in
Gromacs 5.0.4?
In versions 4.5 and 4.6 i used
nstlist = 0
ns_type = simple
pbc = no
This no longer works, as I get the error:
Domain decomposition does not support
On 6/10/15 9:22 AM, soumadwip ghosh wrote:
Thanks Justin,
actually I did look into what you suggested. I
made a carbon nanotube topology with the help of pbd2gmx. Now, the
atomtypes specified in the .rtp file was CA as it is aromatic carbon
atoms. Then I looked into the
Hey Mirco,
Your 1-3% claim is based on the webpage you linked ?
Is it reliable to compare GPU performances for gromacs with those of 3D
videogames ?
Thanks!
2015-06-11 13:21 GMT+02:00 Mirco Wahab mirco.wa...@chemie.tu-freiberg.de:
On 11.06.2015 13:08, David McGiven wrote:
We're finally
On 6/11/15 1:40 AM, soumadwip ghosh wrote:
Hello,
I am asked by one of the reviewers of my paper about the
distribution of ions ( Mg2+) bound to a single stranded DNA as a function
of simulation time at different salt concentrations. In order to do that I
have calculated the RDF of
On 6/11/15 5:53 AM, Jan Jirsák wrote:
Hello everyone,
what is the correct setup for simulations with no PBC and no cuttoffs in
Gromacs 5.0.4?
In versions 4.5 and 4.6 i used
nstlist = 0
ns_type = simple
pbc = no
This no longer works, as I get the error:
Domain decomposition does not support
On 11/06/15 03:59, 范聪 wrote:
Hello, everyone!
I've run two molecular dynamics using gromacs with exactly the same inputs, in the very
same computer, and there's no radom process such as velocity distribution.( I've used
mdrun -t nvt.cpt to stop a new velocity distribution)
Now I'm puzzled
Hi,
On Thu, Jun 11, 2015 at 9:00 AM ashish bihani ashish.bih...@outlook.com
wrote:
I extracted [was instructed to extract] trajectory frames at every 10 ps
from a 10ns xtc file and energy minimized each of them. How do I cluster
them?
I tried to do ls *.gro | gmx cluster -f {.}.gro , did
I extracted [was instructed to extract] trajectory frames at every 10 ps from a
10ns xtc file and energy minimized each of them. How do I cluster them?
I tried to do ls *.gro | gmx cluster -f {.}.gro , did not work.
I concatenated the frames and made an xtc file and tried to cluster it in
Hi all,
I am simulating the organic-water system by using umbrella sampling method.
I would like to extract the solute-solvent and solvent-solvent interactions
information from energy file. In order to do that I need to define energy
groups in .mdp file. My solute is one water molecule and
David van der Spoel spoel@... writes:
Use grid search in any case. It supports vacuum.
Thank you very much, it seems to work. I wonder, does nstlist variable have
any relevance in this case? I mean, here all particles interact with one
another, so it should be sufficient to build neighbor list
Justin Lemkul jalemkul@... writes:
Use mdrun -nt 1
Thank you for a quick reply - however, I really need to parallelize - single
CPU run would take ages;)
Regards, Jan
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Hi,
That particular optimization hasn't been implemented in the multi-domain
case. It's on the table for post 5.1, however.
Mark
On Thu, 11 Jun 2015 17:45 Jan Jirsák janjir...@gmail.com wrote:
David van der Spoel spoel@... writes:
Use grid search in any case. It supports vacuum.
Thank you
Dear Andre,
Many thanks for the message, was very useful. I followed your comments
carefully. Below;
(1) I would suggest you not to take the last frame of the NPT simulation as
the correct volume. You should instead take an average volume from the
equilibrated NPT simulation and then edit
On 09/06/15 17:29, Michael Shirts wrote:
If the simulation are generating configurations with the Boltzmann
probability distribution, the results should the same up to error.
Cv and Cp should not be exactly the same, though for liquids at room
temperature, they are pretty close (look up the
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