[gmx-users] GMX 2020 - COMM Removal Issue

[Daniel Kozuch]

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 <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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