[gmx-users] GMX 2020 - COMM Removal Issue
Paul bauer
paul.bauer.q at gmail.com
Fri Mar 6 19:00:17 CET 2020
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-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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>> Gromacs Users mailing list
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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
>
> ==================================================
>
> --
> 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
>
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--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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