[gmx-users] com motion and position restraints may cause artifacts

[Justin Lemkul]

On 1/17/20 3:01 AM, Berk Hess wrote:
> Hi,
>
> Using center of mass motion removal in combination with an absolute reference in the system, such as position restraints, will always lead to artifacts, as physical motion is removed and not drift due to numerical rounding errors. For the most common case of equilibrating macromolecules using position restraints these artifacts are usually negligible.
>
> So we should probably add a sentence to the note:
> Removing center of mass motion in the presence of positions restraints  might cause artifacts. When position restraints are used to equilibrate a macromolecule these artifacts are usually negligible.

Thanks, Berk. I do think this addition would be important. Most people 
are going to encounter the note doing exactly what you describe, 
equilibrating a macromolecule. If the artifacts are negligible in this 
case, it should be made clear to avoid concern.

-Justin

> I think we should add a comm-removal setting "auto" which should be the default, so grompp can automatically turn off comm-removal when using position restraints.
>
> I realize now that we should check if there are no other artifacts when doing equilibration with position restraints in an NPT ensemble without comm-removal. I expect NVT should be fine without comm-removal.
>
> Cheers,
>
> Berk
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christos Deligkaris <deligkaris at gmail.com>
> Sent: Thursday, January 16, 2020 5:03 PM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] com motion and position restraints may cause artifacts
>
> The ambiguity in the gromacs 2020 note made me concerned, as it was
> not clear to me whether my system (DNA+small molecule) fills in the
> category where artifacts are caused. The gromacs note could have been
> a bit more helpful by referencing specific publications so that we can
> educate ourselves.....
>
> Best wishes,
>
> Christos Deligkaris, PhD
>
> On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 1/16/20 5:17 AM, Alessandra Villa wrote:
>>> Hi,
>>>
>>> On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
>>> wrote:
>>>
>>>> dear all,
>>>>
>>>> I installed gromacs 2020 and I now get the following message during
>>>> equilibration:
>>>>
>>>> NOTE 1 [file nvt.mdp]:
>>>>
>>>>     Removing center of mass motion in the presence of position
>>>> restraints  might cause artifacts
>>>>
>>>> I do not recall seeing this with gromacs 2018. In which cases are
>>>> artifacts created? Is it now recommended to not remove the center of
>>>> mass motion during equilibration?
>>>>
>>>>
>>> It is recommended not to have position restrain and remove of center of
>>> mass at the same moment. That is also the case of the equilibration phase.
>>> That may cause artifact depending on the system and the condition you are
>>> simulating.
>> What is the nature of these artifacts and where is this documented?
>> Combining position restraints with COM motion removal is an extremely
>> common practice. Phrases like "might cause artifacts" are troubling
>> because that implies uncertainty. Are there cases when this combination
>> does not cause artifacts?
>>
>> -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

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