[gmx-users] misunderstanding comm-grps

[Justin Lemkul]

On 2/5/20 5:11 PM, Miro Astore wrote:
> Oh thank you very much I think I got confused looking at older documentation.
>
> What sort of artefacts get created by using
>
> comm-grps = Protein non-Protein?

You're separately subtracting net COM velocities from two species that 
should be treated uniformly. I have seen simulations randomly crash in 
these cases.

-Justin

> On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 2/3/20 7:33 PM, Miro Astore wrote:
>>> Hi everyone,
>>>
>>> I have tried using comm_grps to try and remove center of mass motion
>>> from my system.
>>>
>>> I used the following configuration
>>>
>>> comm_grps               = non-Protein Protein
>>> nstcomm                 = 100
>>> comm_mode               = linear
>>> comm_grps               = non-Protein Protein
>> Don't do this. Multiple COM motion removal groups are only appropriate
>> in layered systems that have different diffusion behavior.
>>
>>
>>>                                     refcoord_scaling        = com
>>>
>>> But I still get considerable drift in my protein. Am I
>>> misunderstanding what comm is actually doing and I should use the
>>> pulling code if I want my protein to stay in the center of the box?
>> Dallas covered this nicely. The algorithm does not (and is not intended
>> to) prevent diffusion. It subtracts erroneous contributions to the
>> kinetic energy in the system.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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

==================================================