[gmx-users] Simulations with SWM4-DP water model in non PBC
David van der Spoel
spoel at xray.bmc.uu.se
Sun Aug 12 08:35:36 CEST 2018
Den 2018-08-11 kl. 16:33, skrev Chi Yuen Pak:
> Dear GROMACS users,
> I would like to ask a question concerning about the simulation of a water droplet, with SWM4-DP polarizable water model in nonperiodic boundary conditions. The GROMACS version I use is 2018.2. I have been only able to successfully run the simulation with only “Group” as the cutoff scheme in non PBC. Multiple OpenMP threads are not supported with “Group”. Also, shell particles are not implemented with domain decomposition, so I have not been able to run the simulation with more than a single core. The following commands are what I use (with thread-MPI)gmx_mpi grompp -f eq.mdp -c em.gro -p swm4-dp.top -r posre.gro -o eq.tprmpirun -np 1 gmx_mpi mdrun -ntomp 1 -deffnm eq
Are you sure it is not using more than one thread? What does it say in
the log file?
> In the paper “Atomistic simulation of ion solvation in water explains surface preference of halides” by Prof. David Van der Spoel in 2011 (doi: 10.1073/pnas.1017903108), they also used the SWM4-DP water model in non PBC (no cutoffs) in GROMACS. I can only guess they used multiple cores for their simulations, or did they? Does anyone know if it is possible to run multiple cores to simulate SWM4-DP in non PBC?
That was run with gromacs 4.6 using the -pd option.
You could do that as well of course.
> Attached are the mdp setting and topology for your reference.Thanks.
> Best,Chi Yuen
> mdp setting: https://www.dropbox.com/s/e1sord21slgn084/eq.mdp.pdf?dl=0
> topology: https://www.dropbox.com/s/0gj8ot2m6k8b019/swm4-dp.top.pdf?dl=0
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
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