[gmx-users] GMX 2020 - COMM Removal Issue
Daniel Kozuch
dkozuch at princeton.edu
Fri Mar 6 20:35:58 CET 2020
Thanks Paul! Unfortunately while 2020.1 seems to work for the membrane system (no protein), for the protein-membrane system I am still having significant COM motion in the xy plane (i.e. the membrane translates several nm/ns sideways in its own plane). This happens regardless of coupling the membrane and protein independently (3 COMM groups: protein, membrane, solvent) or together (2 COMM groups: protein-membrane, solvent). Any suggestions on how to track down why a protein imbedded in the membrane is causing this problem?
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 Paul bauer
Sent: Friday, March 6, 2020 1:02 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] GMX 2020 - COMM Removal Issue
Hello,
we resolved some issues with COM removal in the latest release (please see the patch notes for more details).
So it might be that you where affected by this before.
Please let us know if the issue shows up again.
Cheers
Paul
On 06/03/2020 18:58, Daniel Kozuch wrote:
> Additional (good) news, the problem appears to be resolved in the 2020.1 update (at least for the membrane only system). I'll conduct some additional tests to see if there is any lingering problems.
>
> 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-Se
>>> p
>>> 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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> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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