[gmx-users] Shear flow with deform option

2017-09-05 Thread Makoto Yoneya
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

Re: [gmx-users] Ionic liquid simulation problem.

2017-09-05 Thread Justin Lemkul
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

Re: [gmx-users] HPC performance in Gromacs ?

2017-09-05 Thread Szilárd Páll
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

Re: [gmx-users] Gromacs 2016.3 FLOATING-POINT EXECPTION/DIVIDE-BY_ZERO errors

2017-09-05 Thread David van der Spoel
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:

Re: [gmx-users] Ionic liquid simulation problem

2017-09-05 Thread soumadwip ghosh
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

[gmx-users] HPC performance in Gromacs ?

2017-09-05 Thread Li, J.
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

[gmx-users] Fwd: Ionic liquid simulation problem.

2017-09-05 Thread Ednilsom Orestes
*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*

[gmx-users] Ionic liquid simulation problem.

2017-09-05 Thread Ednilsom Orestes
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

Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

2017-09-05 Thread serpercon
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

Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

2017-09-05 Thread Mark Abraham
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

[gmx-users] Gromacs 2016.3 FLOATING-POINT EXECPTION/DIVIDE-BY_ZERO errors

2017-09-05 Thread Rainer Rutka
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

[gmx-users] Gromacs 2016.3 FLOATING-POINT EXECPTION/DIVIDE-BY_ZERO errors

2017-09-05 Thread Rainer Rutka
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

Re: [gmx-users] HPC performance in Gromacs ?

2017-09-05 Thread Nikhil Maroli
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[gmx-users] HPC performance in Gromacs ?

2017-09-05 Thread Li, J.
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