[gmx-users] center the system on specific atoms type

[Tsjerk Wassenaar]

Hey :)

There's a suggested trjconv workflow at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

T.

On Thu, Mar 15, 2012 at 11:41 AM, R.Perez Garcia
<r.perez.garcia at student.rug.nl> wrote:
> Dear Tsjerk,
> Thank you for your answer!
> I dont like trouble, so, Ii will leave comm_grps =  System...
> But, could you spare some comments how to center it afterwards? I dont know
> why but the fullerene like to spend a lot of time in the boundary (i.e.
> divided in two, where it is difficult to see).
> Best regards: R
>
>
> On 15-03-12, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> Hey :)
>
> Why would you want to keep it constant? It's asking for trouble. The
> fluctuations in a small part of the system like a fullerene molecule
> can be pretty large. If you try to correct the VCM of that bit only,
> you make it constantly bump into your solvent molecules. Especially if
> you have nstcomm = 10 or so, the shift may be considerable, and you
> may cause overlaps and crash your system. And that while it's so easy
> to center on the fullerene afterwards!
>
> Cheers,
>
> Tsjerk
>
> On Thu, Mar 15, 2012 at 11:16 AM, R.Perez Garcia
> <r.perez.garcia at student.rug.nl> wrote:
>>  Dear all,
>> I am running a simulation in of a fullerene in different solvents. I would
>> like to keep the fullerene somehow centred in the box, so I changed co
>> comm_grps =  System to mm_grps  =  FUL.
>> If I do this the following error pop up:
>>
>> There are:   395      Other residues
>> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
>> into groups...
>>
>> NOTE 1 [file short1.mdp]:
>>   4728 atoms are not part of any of the VCM groups
>>
>> WARNING 1 [file short1.mdp]:
>>   Some atoms are not part of any center of mass motion removal group.
>>   This may lead to artifacts.
>>   In most cases one should use one group for the whole system.
>>
>> I am not sure if it is possible to tackle this....
>> Any suggestion would be welcomed.
>> Best regards: R
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands