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

madisonw at zju.edu.cn madisonw at zju.edu.cn
Thu Aug 2 04:06:39 CEST 2018

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

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? 



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