[gmx-users] Gromacs for reverse transformation

[shivangi nangia]

Hello Tsjerk,

Is there any example/tutorial on how to use the backward apart from the
notes in the initram.sh

Thanks,
sxn




On Thu, May 22, 2014 at 1:41 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.ziphelp
> > 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
> > > > --
> > > > Gromacs Users mailing list
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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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