[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc file

leila karami karami.leila1 at gmail.com
Mon Jan 3 18:39:19 CET 2011

Dear Tsjerk

thanks for your reply

I have not experience in using python.

in [python -c 'r,a,b,c=range,1868,24086,24100;open("r.ndx","w").write("[x]\n"+"\n".join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'].

r.ndx contains all the atoms. is it true?

why did you use r,a,b,c=range,1868,24086,24100.

is r,a,b,c=range,1867,24085,24099 wrong?


Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group

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