[gmx-users] how to remove periodicity when using g_rmsd

[Florian Haberl]

Hi,
On Thursday, 27. September 2007 11:29, TANG JIAOWEI wrote:
> Dear all,
> I am studying on a big protein with 16 subunits and when i used g_rmsd to
> one subunit of the protein, the result seems strange that the structure of
> the subunit changes much but it should not.. I searched the mailing list
> and it may be caused by the periodic thing. Could you tell me how to remove
> the periodic thing in detail before i use g_rmsd.

something like:

trjconv -s yourmdstartfile.tpr -f yourtrj.trr -o pbc.trr -pbc nojump

select as group your complete system.

than g_rmsd ...

>
> Thank you
>
> Tang jiaowei


Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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