[gmx-users] how to center the molecule with trjconv

[Zhenyu Meng]

Hi Justin,
Thanks for your comments, it's a big help.

2015-07-15 21:32 GMT+08:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/14/15 11:20 PM, Zhenyu Meng wrote:
>
>> Dear GROMACS users,
>> I want to simulate DNA in a cubic box with water as solvent and visualize
>> it.
>> By using -pbc mol I can see part of the DNA is out of the box so I want to
>> center the DNA in box.
>> But using -center seems destruct the DNA into several parts. I tried to
>> use
>> -pbc mol followed by -center or -center followed by -pbc mol but both
>> cannot center the DNA (the DNA doesn't fall apart but it's still not in
>> the
>> center).
>> I'm curious about the algorithm about -center option. e.g. if I have a pbc
>> cubic box with length of 5, and the COM of the DNA is at (3,3,3), in that
>> way, if I use -center I think all the atoms of the system(including DNA
>> and
>> water) will shift with a vector(-0.5,-0.5,-0.5) to make sure the COM of
>> DNA
>> is now at(2.5,2.5,2.5) (the default boxcenter). Am I correct?
>> Your help will be highly appreciated!
>>
>>
> For multi-chain molecules it is often helpful/necessary to center on one
> chain using an index group.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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-- 
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University