[gmx-users] COM motion removal: diffusion analysis

[gromacs query]

>> It is not a matter of resetting positions; it is about subtracting
falsely accumulated kinetic energy.

Thanks, this is it :)

On Mon, Dec 28, 2015 at 8:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/28/15 10:28 AM, gromacs query wrote:
>
>> Hi All
>>
>>
>> I have protein-membrane system and gromacs tutorial by Justin suggests to
>> do COM separately for protein_membrane and water. I am bit meesed up COM
>> removal understanding.
>>
>>
>> 1) I want to do diffusion analysis of protein in a membrane (2D/3D) how it
>> will influence my results if I perform it on a trajectory with COM removal
>> as seperate groups or on trajectory with COM removal of system.
>>
>>
> The reason that interfacial systems are treated this way is because the
> diffusion of the two interfaces is different, hence must be treated
> separately.
>
> 2) Is it possible to remove COM seperately on a trajectory created using
>> COM removal on system. e.g. for msd calculation one can use -rmcomm
>>
>>
> IIRC the use of -rmcomm should have no effect if COM motion removal was
> already applied during the simulation.
>
> 3) May be am wrong here: In case of simple peptide in water box, and I
>> remove COM for peptide and water (NOT as whole system) then in this case
>> peptide should not cross the unit box. Is it right?
>>
>>
> For a simple solute in solvent, you should not separate groups (I have
> even seen this result in crashes before).  COM motion removal is used to
> counteract spurious accumulation of translational kinetic energy as a
> result of using thermostats.  Read about the old "flying ice cube"
> problem.  It is not a matter of resetting positions; it is about
> subtracting falsely accumulated kinetic energy.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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