[gmx-users] fraction of native contacts calculation

[bipin singh]

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
> >
> > ========================================
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> -----------------------------------------------
> 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
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
-----------------------
*Regards,*
Bipin Singh