[gmx-users] Number of SOL/Water in gmx_moltype_t

[Pradip Biswas]

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