[gmx-users] Gromacs for reverse transformation

[shivangi nangia]

Thanks a lot Tsjerk.


Thanks,
Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut


On Thu, May 22, 2014 at 11:01 AM, 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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