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

[Mark Abraham]

You can't take an OHN out of the coordinate file and not out of the
topology and produce a .tpr. Production of a .tpr requires that the
[molecules] field matches the coordinate file.

When you do have a .tpr, you are looking at *moltype*. This is the
internal representation of the [moleculetype]. It is not a global dump
of the system contents - there isn't one, either.

Mark

On Wed, Aug 21, 2013 at 3:15 AM, Pradip Biswas <biswas.pk at gmail.com> wrote:
> 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
>> > --
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>
>
>
> --
> 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
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