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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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