[gmx-users] Gromacs for reverse transformation

[Tsjerk Wassenaar]

Hi Chandan,

You may have to write a mapping file, as explained in one of the tutorials
in the supplementary information of the paper. If that poses problems, you
can contact me. I may be interested in adding new mappings :)

Cheers,

Tsjerk
On May 22, 2014 6:42 PM, "Chandan Choudhury" <iitdckc at gmail.com> wrote:

> Hi Tsjerk,
> Do the scripts available in the backward.zip file
> http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help
> me to backmap a coarse-grained polymer?
>
> Chandan
>
>
> On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi sxn,
> >
> > I would argue that that method for reverse transformation is largely
> > obsolete. Please have a look at
> > http://www.cgmartini.nl/cgmartini/index.php/back
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> > <shivangi.nangia at gmail.com>wrote:
> >
> > > Hello,
> > >
> > > I want to do a reverse transformation of my system containing:
> bi-layer,
> > > protein and water.
> > >
> > > The Martini website (
> > > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says
> > to
> > > install gromacs version 3.3.1
> > >
> > > I am currently using 4.6.1 gromacs version.
> > >
> > > ques A: Is this version incapable of the transformation?
> > >
> > > Also, the martini website says to:
> > >
> > > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that
> > > contains all necessary gromacs files for this exercise.*
> > >
> > > *2. Compile and/or source the modifi ed version of gromacs (remember
> this
> > > tool is based upon gromacs version 3.3.1 and needs the corresponding
> > tricks
> > > and threats to be compiled.)*
> > >
> > > *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> > >
> > >
> > > ques B:On performing untar on rev_trans.tar.gz there is no
> > MARTINITUTORIAL
> > > directory
> > > ques C: On performing untar on gmx_rev.tar.gz there is no bin folder
> > >
> > > KIndly help.
> > >
> > > Thanks,
> > > sxn
> > > --
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
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