[gmx-users] About center of mass removal

[Justin A. Lemkul]

rama david wrote:
> Hi Gromacs Friends,
> Thank you for your reply and nice suggestion.
> I read the wikipedia article 
> ..http://en.wikipedia.org/wiki/Flying_ice_cube suggested by Mark..
> 
> as per the article..
> More conservatively, the rate of velocity rescaling can be reduced, the 
> scale factor computed over a time-averaged sample of instantaneous 
> temperatures, or an alternative means of thermostatting such as the 
> Nosé-Hoover thermostat 
> <http://en.wikipedia.org/wiki/Nos%C3%A9-Hoover_thermostat> can be used.
> 

The wording of this section is unclear to me.  I am not certain whether the use 
of the N-H thermostat removes or simply reduces the flying ice cube effect.  In 
either case, I wouldn't rely on a thermostat to solve the issue.

> So I used the Nose-Hover thermostat..
> after finished mdrun , to see movie I used the command trjconv -s ..tpr 
> -f ...xtc -pbc nojump -o protein.pdb -dt 10 -center
> I found that after these command also my molecule some time moving the 
> out of box ..Is it right???
> 

There is no such thing as "outside" and "inside" a periodic box.  Please see:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

>  In these MD run I not remove COM(center of motion) so I want to check 
> it is
> not producing any misleading  and run is not wrong (No flying ice cube 
> effect)..??
> 
>   the grommp warning was like ..
> 
> 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
>  And I used Maxwarn 1... So Now I want to check is these warning
> affect my run ...which proparty I have to check ??

I still see no justifiable reason for you to turn off COM motion removal.  Why 
do you think you need to do this?

In any case, as the Wikipedia page describes, there will be a buildup of kinetic 
energy (i.e. it will increase) and intramolecular motion (i.e. bonded terms) 
will "freeze" such that the molecules move as a rigid body.  You should be able 
to measure energies for these terms very easily or otherwise observe the 
phenomenon.

This is an old problem with a straightforward solution.  I'd suggest you use it:

comm_mode = Linear
nstcomm = 1
comm_grps = System

-Justin

> Thank you in advance..
> 
> On Sat, Mar 24, 2012 at 9:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     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
>     <http://en.wikipedia.org/wiki/Flying_ice_cube>
> 
>     Mark
>     -- 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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