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

[Pradip Biswas]

What about OHN - the hydroxyl radical? I put two of them in the system to
understand the issue. Under DNA_chain_X, you clearly see nr=2 for OHN. If I
take one OHN out from pdb (means one DTMP, one OHN and water), I again get
nr=1 for OHN.

residue (2):
>       residue[0]={name="DTMP", nr=1, ic=' '}
>       residue[1]={name="OHN", nr=2, ic=' '}

Pradip


On Tue, Aug 20, 2013 at 3:12 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
P. K. Biswas, PhD
Laboratory of Computational Biophysics & Bioengineering
Associate Professor of Physics
Tougaloo College
601-977-7788