[gmx-users] how to remove periodicity when using g_rmsd
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Thu Sep 27 11:40:53 CEST 2007
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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