[gmx-users] About center of mass removal

[Mark Abraham]

On 24/03/2012 11:06 PM, rama david wrote:
> Hi Gromacs Specialist,
>                  I want to study How the protein interact
> with each other ??

Great, but whether or not you remove center of mass translation *of the 
whole system* has nothing directly to do with it.

>   I run one simulation with  following MDP file option ..
> comm_mode               = Linear                ; remove center of 
> mass translation
> nstcomm                 = 1                     ; [steps] frequency of 
> mass motion removal
> comm_grps               = Protein Non-Protein   ; group(s) for center 
> of mass motion removal
>
>
> Now I decided to remove the center of mass
> with following option .........

Changing this option to "None" doesn't "remove the center of mass", it 
stops removing the motion of the center of mass.

> comm_mode               = None                  ; remove center of 
> mass translation
> nstcomm                 =                       ; [steps] frequency of 
> mass motion removal
> comm_grps               =                       ; group(s) for center 
> of mass motion removal
>
> I got the following warning at the  command grompp...
>
>  WARNING 1 [file md.mdp]:
>   You are not using center of mass motion removal (mdp option comm-mode),
>   numerical rounding errors can lead to build up of kinetic energy of the
>   center of mass
>
> I run with maxwarn 1 , Is I am right??

Do you know why you can ignore this warning? If not, do not use -maxwarn.

>
> What Is  reason for above error??

You're getting a warning because you are doing something that might be 
wrong - in fact, likely to be wrong. See 
http://en.wikipedia.org/wiki/Flying_ice_cube

Mark