[gmx-users] fraction of native contacts calculation

[Sanku M]

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