[gmx-users] GMX 2020 - COMM Removal Issue

[Daniel Kozuch]

Yes, a smaller system with only membrane/solvent (no protein) causes the same issue.

Best,
Dan

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin Lemkul
Sent: Friday, March 6, 2020 11:02 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue



On 3/6/20 10:00 AM, Daniel Kozuch wrote:
> [Somehow my response got put in a different thread - hopefully this 
> works]
>
> Justin,
>
> Thanks for your reply. I agree that some COM motion is normal. 
> However, 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.

Does a membrane system (no protein) also cause the same issue?

-Justin

> Best,
> Dan
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se 
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of 
> Justin Lemkul
> Sent: Tuesday, March 3, 2020 3:02 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue
>
>
>
> 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-Sep
>> t
>> ember/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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--
==================================================

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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