[gmx-users] Crash of DD with periodic_molecules

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

[gmx-users] Vacuum simulation in Gromacs 5

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

Re: [gmx-users] problem using grompp

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

Re: [gmx-users] Clustering energy minimized equally space frames

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

Re: [gmx-users] problem using grompp

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

Re: [gmx-users] Clustering energy minimized equally space frames

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

[gmx-users] problem using grompp

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

Re: [gmx-users] energy groups definition

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

[gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?

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.

Re: [gmx-users] why gromacs cannot repeat out the results?

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

Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?

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 ?

Re: [gmx-users] problem using grompp

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

Re: [gmx-users] Vacuum simulation in Gromacs 5

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

Re: [gmx-users] regarding SwissParam topology

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

Re: [gmx-users] Performance of NVIDIA GTX980 in PCI-e 3.0 x8 or x16 slots ?

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

Re: [gmx-users] Ion binding to DNA

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

Re: [gmx-users] Vacuum simulation in Gromacs 5

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

Re: [gmx-users] why gromacs cannot repeat out the results?

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

Re: [gmx-users] Clustering energy minimized equally space frames

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

[gmx-users] Clustering energy minimized equally space frames

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

[gmx-users] energy groups definition

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

Re: [gmx-users] Vacuum simulation in Gromacs 5

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

Re: [gmx-users] Vacuum simulation in Gromacs 5

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 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Vacuum simulation in Gromacs 5

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

Re: [gmx-users] Different Cv and Cp

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

Re: [gmx-users] Different Cv and Cp

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