Re: [gmx-users] A question about simulation system includes more than 100000 atoms using Gromacs

Hi Zhuquing, as far as I know, atom numbers in .gro file are irrelevant - gromacs asigns indices based on the order of records in the file. I my configurations numbers are often quite random, as I copy and paste coordinates from different sources. It never caused any problems in gromacs

Re: [gmx-users] Location of Bubbles.

Hi Sujith, you can try to translate the initial configuration by, say, L/2 in all directions using trjconv. If the bubble appears again at the edge, I would suspect artifacts. If you are using Verlet cutoff scheme, you can also try to change it to group - it helped in my simulation when a droplet

[gmx-users] Strange behavior of water droplet on a solid surface with Verlet cutoff scheme in GMX 5.0.4

Dear community, I simulate a droplet made of rigid SPC waters (ca 1 molecules) lying on a solid surface placed at z=0 represented by LJ atoms with fixed coordinates. Using cutoff-sheme = Verlet with quite long cutoff (3.0nm) produces a strange spurious force, which seems to pull the droplet

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

. Regards, Jan 2015-06-15 21:51 GMT+02:00 Szilárd Páll pall.szil...@gmail.com: On Sun, Jun 14, 2015 at 6:54 PM, Jan Jirsák janjir...@gmail.com wrote: Hi, I did the test and found out that -nt 8 is even slower than -nt 1 !! FYI: -nt is mostly backward compatibility option and for clarity it's best

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

of details as normally? This is what people do in the plane-wave codes when the so-called 'cluster representation' is desired. On Sun, Jun 14, 2015 at 1:54 PM, Jan Jirsák janjir...@gmail.com wrote: Hi, I did the test and found out that -nt 8 is even slower than -nt 1 !! However, I think

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

people do in the plane-wave codes when the so-called 'cluster representation' is desired. On Sun, Jun 14, 2015 at 1:54 PM, Jan Jirsák janjir...@gmail.com wrote: Hi, I did the test and found out that -nt 8 is even slower than -nt 1 !! However, I think that simulation hasn't even properly

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

Hi, I did the test and found out that -nt 8 is even slower than -nt 1 !! However, I think that simulation hasn't even properly started with 8 threads and got stuck somewhere in the beginning. Details: I used a short run (1000 steps) for testing. mdrun -nt 1 finished after ca 11 hours, whereas

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

Hi, I have one more problem with running this system with thread-MPI (tested in both 5.0.4 and 5.0.5 on two different machines). When I set everything as you advised me, it runs, however top command shows only 100% load - i.e., only single CPU is used (and it is really very very slow), despite

[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] 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