[gmx-users] fraction of native contacts calculation

[bipin singh]

Thanks a lot Sanku for your help.

On Thu, Nov 1, 2012 at 11:38 PM, Sanku M <msanku65 at yahoo.com> wrote:

> Bipin,
>   There might be a workaround. You might want to check out Plumed plugin
> in latest versions of VMD for calculating fractions of native contact. You
> can load the gromacs trajectory along with the native .gro file in VMD and
> use Plumed plugin inbuilt in VMD . You need to install plumed most probably
> early.
>
>
>
> ________________________________
>  From: bipin singh <bipinelmat at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, November 1, 2012 1:23 PM
> Subject: Re: [gmx-users] fraction of native contacts calculation
>
> Thanks for your response. Hope to see this feature in upcoming GROMACS
> release. Before that, could it be possible to get the modified code in the
> user contribution section, it may be useful for many GROMACS users.
>
>
> On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> wrote:
>
> >
> > 31 okt 2012 kl. 13.43 skrev Justin Lemkul:
> >
> > >
> > >
> > > On 10/31/12 6:02 AM, bipin singh wrote:
> > >> Hello all,
> > >>
> > >> Is there any way to calculate fraction of native contacts during the
> > >> simulation in gromacs. I searched the archives but didn't found any
> > >> significant clue.
> > >
> > > At present, there is no way to do this.  Likely one could modify the
> > g_mindist code to do this - it would be a very nice feature.
> > >
> >
> > If one could get the -sel option of g_hbond to work again then you would
> > get such information with -contact.
> >
> > Erik
> >
> >
> > > -Justin
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > --
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> > -----------------------------------------------
> > Erik Marklund, PhD
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,    75124 Uppsala, Sweden
> > phone:    +46 18 471 6688        fax: +46 18 511 755
> > erikm at xray.bmc.uu.se
> > http://www2.icm.uu.se/molbio/elflab/index.html
> >
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>
>
> --
> -----------------------
> *Regards,*
> Bipin Singh
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-- 
-----------------------
*Regards,*
Bipin Singh