[gmx-users] About center of mass removal

[rama david]

Hi Gromacs Friends,
Thank you for your reply and nice suggestion.
I read the wikipedia article
..http://en.wikipedia.org/wiki/Flying_ice_cubesuggested 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.

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???

 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 ??
Thank you in advance..

On Sat, Mar 24, 2012 at 9:41 PM, Mark Abraham <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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