[gmx-users] Gromacs for reverse transformation

[Tsjerk Wassenaar]

Hi sxn,

The paper describing the method has a tutorial as supplementary material.
It's also available from our site at the University of Erlangen, but I'l
have to look up the address. In addition, Alex de Vries from Groningen
recently developed another tutorial for a hands-on session he arranged. Not
sure if it is available online, I'll ask him to seenif we can add it to the
backward site at cgmartini.nl.

Cheers,

Tsjerk
On May 22, 2014 9:28 PM, "shivangi nangia" <shivangi.nangia at gmail.com>
wrote:

> 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
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > >
> > > --
> > > Chandan Kumar Choudhury
> > > National Chemical Laboratory, Pune
> > > India
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>