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

[leila karami]

Dear Justin and Chris

very thanks for your reply and guidance.

I did all the steps successfully. then I used (./my_tool -f final.xtc -o
final.pdb -b 300 -e 350), the final.pdb file was created without problem.
when I opened final.pdb file by text editor, order of waters and ions in
final.pdb was like final.xtc (waters are before ions).
my purpose was 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)

but this wasn't done. Is there problem in modification made in gmx_trjconv.c
or same my_tool.c file:

####### Now go to line 1264 of the file and replace this:

               for(i=0; i<nout; i++) {
                 copy_rvec(fr.x[index[i]],frout.x[i]);
                 if (bVels && fr.bV) {
                   copy_rvec(fr.v[index[i]],frout.v[i]);
                 }
                 if (bForce && fr.bF) {
                   copy_rvec(fr.f[index[i]],frout.f[i]);
                 }
               }

####### with this:

               for(i=0; i<=1866; i++) {
                 copy_rvec(fr.x[index[i]],frout.x[i]);
               }
               for(i=24085; i<=24098; i++) {
                 copy_rvec(fr.x[index[i]],frout.x[i-22218]);
               }
               for(i=1867; i<=24084; i++) {
                 copy_rvec(fr.x[index[i]],frout.x[i+14]);
               }

               for(i=0; i<nout; i++) {
                 if (bVels && fr.bV) {
                   copy_rvec(fr.v[index[i]],frout.v[i]);
                 }
                 if (bForce && fr.bF) {
                   copy_rvec(fr.f[index[i]],frout.f[i]);
                 }
               }
             }




-- 

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