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

[Mark Abraham]

residue is a sub-field of moltype, so you are seeing that there is
indeed one SOL residue per water molecule, as expected. Look elsewhere
and you will see that there are 351 of those molecules recorded. The
same is true of the DNA chain, but since there's only one DNA chain,
the number of residues per molecule coincides with the number in the
system.

Mark

On Tue, Aug 20, 2013 at 7:48 PM, Pradip Biswas <biswas.pk at gmail.com> wrote:
> 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
> --
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