Dear GROMACS users:
The GROMACS manual says that the off-diagonal elements (of deform option) can
be used to shear a solid or a liquid.
Then, how should I set the "comm-mode" option (concern for removing center of
mass translation) to get shear flow with this deform option?
I'd tried
On 9/5/17 2:32 PM, Ednilsom Orestes wrote:
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:
1. Prepared the respective PDB files and added/modified
Hi,
Only one of the files has the right permissions, but based on that the
TL;DR conclusion is that you seem to be oversubscribing the nodes and
missing thread pinning.
You're also running at a fairly high parallelization (17700 atoms system on
72 cores across 3 nodes) and to get good performance
On 05/09/17 11:54, Rainer Rutka wrote:
HI!.
My name is Rainer. I am one of the module-/SW-maintainers
for the bwHPC-C5-project. "http://www.bwhpc-c5.de/en/index.php;
Since a couple of time we can't run Gromacs 2016.n on
our clusters. Here's one of the errors we received from
one of the users:
Hi,
I am not sure why you used the gmx solvate command for putting the
anionic species in your simulation box. It is meant for filling up the
simulation box with water molceules as the resname 'SOL' in the
topol.top file. Thus when you hit grompp it expects 'SOL' entry in
your topology file, cant
Hello Nikhil,
Thanks for your suggestions. here is the links for two log files. 1 is for
normal set, 2 is for tunning set.
https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYbEY2dUFvS3pLUWs/view?usp=sharing
https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYcjctSHBOckRKeEU/view?usp=sharing
*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*
*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic
liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
the following protocol:
1. Prepared the respective PDB files and added/modified the OPLS/AA force
field parameters updating
Hello,
My apollogies, the drift is present whether I use tabulated potentials
or not. The email's title I chose is misleading. If I am not mistaken I
am using a buffer when I put rcut= 1.0 and rlist=1.3 , but this was not
entirely clear to me using with the manual.
Sergio
El 05/09/2017
Hi,
Your earlier email implied that the drift was present when you used the
group cutoff-scheme, whether or not you used tabulated interactions. But
just now you implied something different. Unbuffered cutoffs with the group
scheme are not comparable with e.g. the default buffering used with the
HI!.
My name is Rainer. I am one of the module-/SW-maintainers
for the bwHPC-C5-project. "http://www.bwhpc-c5.de/en/index.php;
Since a couple of time we can't run Gromacs 2016.n on
our clusters. Here's one of the errors we received from
one of the users:
I am using Gromacs on BwUniCluster for
HI!.
My name is Rainer. I am one of the module-/SW-maintainers
for the bwHPC-C5-project. "http://www.bwhpc-c5.de/en/index.php;
Since a couple of time we can't run Gromacs 2016.n on
our clusters. Here's one of the errors we received from
one of the users:
I am using Gromacs on BwUniCluster for
log file.?
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Hello all,
I have a report as following, but I do not have any clear clue about what I
have to do. If I change some default values for -dd/-dds/..., what I should
expect and what I should be careful about about tunning these parameters?
It said the load imbalance is from inhomogeneous. But I am
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