[gmx-users] Simulations with SWM4-DP water model in non PBC
Chi Yuen Pak
chiyuen0622 at yahoo.com.hk
Sat Aug 11 17:04:14 CEST 2018
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
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?
Attached are the mdp setting and topology for your reference.Thanks.
mdp setting: https://www.dropbox.com/s/e1sord21slgn084/eq.mdp.pdf?dl=0
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