[gmx-users] question about the center of mass motion removal

[Justin Lemkul]

On 8/1/18 10:06 PM, madisonw at zju.edu.cn wrote:
> Hello GROMACS users,
>
>
>
> I have a quick question about comm-grps. I want to study the protein dynamics in water with no consideration of diffusion.
>
> The manual suggests me to use groups in removing the center of mass motion by saying that it makes sense to use the same groups for temperature coupling and center of mass motion removal. But some people suggest using the whole

Where does it say that?

> system for center of mass motion removal, such as https://www.mail-archive.com/gmx-users@gromacs.org/msg30001.html.

I stand by what I said there. For a protein in water, use "comm-grps = 
System" (which is the default behavior).

-Justin

> My t-couple and COM motion removal settings are as follows.
>
> ; Temperature coupling is on
> tcoupl= V-rescale            ; modified Berendsen thermostat
> tc-grps= Protein Non-Protein; two coupling groups - more accurate
> tau_t= 0.1  0.1           ; time constant, in ps
> ref_t= 310   310           ; reference temperature, one for each group, in K
>
> ; COM motion removal
> ; These options remove motion and rotation of the protein relative to the solvent/ions
> nstcomm= 100
> comm-mode= linear
>
>
>
> How to set up the grouping properly for my case?
>
>
>
>
>
>
>
> Best,
>
> Wukai

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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