[gmx-users] Regarding creation of mixture of molecules..

[Mark Abraham]

Hi,

No, I can't, I've never done it. Making a box.of  mixed solvent is
something you can find detailed instructions to do, so please do us the
courtesy of googling and trying before asking for more of people's time.
Specific questions are much more likely to get useful answers. :-)

Mark

On Sun, 19 Feb 2017 20:11 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> couldnt get u mark..
> can u kindly elaborate it..in detail..kindly..
>
>
>
>
>   <https://mailtrack.io/>Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> On Mon, Feb 20, 2017 at 12:25 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You choose a suitable force field, use the tools that suit it to
> generate a
> > topology and/or parameters. Then make a mixture using any of various
> > techniques, including the one google will find on the Gromacs webpage.
> Then
> > make sure all the residue naming and atom ordering matches - but this is
> > the easiest part!
> >
> > Mark
> >
> > On Sun, 19 Feb 2017 10:21 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> >
> > how can i create a mixture of molecules in avogadro software and save it
> as
> > .pdb
> > ex. mixture of ammonia and water...
> > and wht r the residues for ammonia and water...?
> > and wht r the forcefeild tht i need tto search these mixtures..??
> > Or create a mixture using any other software..?
> > and get the proper residue to create a topology file in gromacs
> >
> >
> >   <https://mailtrack.io/>Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> > referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> >
> > On Fri, Feb 17, 2017 at 4:27 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> > wrote:
> >
> > > how can i create a mixture of molecules in avogadro software and save
> it
> > > as .pdb
> > > ex. mixture of ammonia and water...
> > > and wht r the residues for ammonia and water...?
> > > and wht r the forcefeild tht i need tto search these mixtures..??
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Research Scholar,
> > > Department of Chemistry, NITK.
> > >
> > >
> > >
> > >   <https://mailtrack.io/>Sent with Mailtrack
> > > <
> > https://mailtrack.io/install?source=signature&lang=en&
> > referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> > >
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Research Scholar,
> > Department of Chemistry, NITK.
> > --
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> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
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