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

[leila karami]

Dear gromacs users

My simulation system contains protein, dna, water molecules and Na+
ions respectively.

I want to reorder water molecules with Na+ ions in final xtc file as

at first

1-1867                       complex (protein and dna)
1868 - 24085              SOL (water molecules)
24086 - 24099            Na+ (ions)

after reordering

1-1867                       complex (protein and dna)
1868 -1881                 Na+ (ions)
1882 - 24099              SOL (water molecules)

How to do that?

I need to this reordering to obtain amber trajectory file (mdcrd) by VMD.

any help and suggestion will highly appreciated.

-- 


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