Hi,
I am using v-4.5.5. I have a system of DNA nucleotide & *two* OH radicals
solvated in water.
The topology file has the following records in the end:
[ molecules ]
; Compound #mols
DNA_chain_X 1
SOL 351
However, when I did gmxdump after running grompp, I see the following:
moltype (0):
name="DNA_chain_X"
...............
...............
residue (2):
residue[0]={name="DTMP", nr=1, ic=' '}
residue[1]={name="OHN", nr=2, ic=' '}
moltype (1):
name="SOL"
..........
..........
residue (1):
residue[0]={name="SOL", *nr=1*, ic=' '}
Aren't we recording the number of solvent residues? I was expecting nr=351
for SOL; the number of water molecule I have in the system. As I get nr=2
for OHN
Thanks,
Pradip Biswas
--
P. K. Biswas, PhD
Laboratory of Computational Biophysics & Bioengineering
Associate Professor of Physics
Tougaloo College
601-977-7788
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
