[gmx-users] GMX 2020 - COMM Removal Issue

[Justin Lemkul]

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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