I agree, but this was a very short simulation (1 ns), so the size of the drift (several nm) was unexpected. To test, I repeated the simulation with GROMACS 2019.6 using all the same settings (but without the new ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don't see the same drift.
Best, Dan On Tue, Mar 3, 2020 at 3:03 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/2/20 9:53 PM, Daniel Kozuch wrote: > > Hello, > > > > I am experimenting with GROMACS 2020. I have compiled the mpi threaded > > version and am using the new settings > > (GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU) as > > suggested on at the following link: > > > https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/ > . > > I am running mdrun with the suggested options: > > "-pin on -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400" on 4 GPUs and > > 28 CPUs with "-ntmpi 4 -ntomp 7". > > > > I am currently running a membrane system with a transmembrane protein in > > water solvent. I am using the following settings for COM removal: > > > > comm_mode = linear > > comm_grps = PROT_MEMB SOL_ION > > > > Here I choose to couple the the protein and the membrane from the advice > in > > this thread: > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108584.html > > > > Unfortunately, I still see a large drift in the z-dimension for the > entire > > membrane/protein group. Currently I have nstcalcenergy/nstcomm set to > 100, > > as decreasing them leads to poor performance. (Hopefully it is > unnecessary > > to set them to 1) > > Removing artificial contributions to COM motion does not mean that the > entities cannot diffuse over time. Depending on the length of your > simulation, drift in absolute position can be perfectly normal. > > -Justin > > > Does anyone have suggestions for avoiding the COM drift? I know this > issue > > has been discussed before (https://redmine.gromacs.org/issues/2867) but > it > > looks like it was resolved in earlier GROMACS versions. As a note, I am > > using a CHARMM force field with CMAP dihedrals. > > > > > > Here are some other potentially relevant mdp options (from CHARMM) in > case > > they help: > > > > integrator = md > > dt = 0.002 > > nstcalcenergy = 100 > > ; > > cutoff-scheme = Verlet > > nstlist = 20 > > rlist = 1.2 > > coulombtype = pme > > rcoulomb = 1.2 > > vdwtype = Cut-off > > vdw-modifier = Force-switch > > rvdw_switch = 1.0 > > rvdw = 1.2 > > ; > > tcoupl = v-rescale > > tc_grps = PROT_MEMB SOL_ION > > tau_t = 1.0 1.0 > > ref_t = 303.15 303.15 > > ; > > pcoupl = Berendsen > > pcoupltype = semiisotropic > > tau_p = 5.0 > > compressibility = 4.5e-5 4.5e-5 > > ref_p = 1.0 1.0 > > ; > > constraints = h-bonds > > constraint_algorithm = LINCS > > continuation = yes > > > > Best, > > Dan > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.