As Justin implied, -merge could potentially make a factor of 2. Try
g_hbond -nomerge.
Erik
On Mar 4, 2013, at 4:02 PM, bipin singh wrote:
Thanks for the reply.
The difference is almost double, through g_hbond the average number of
contacts are 1821 and through g_mindist it is 3643. The calculation
group
does not contains hydrogen atoms.
On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/4/13 9:08 AM, bipin singh wrote:
Hi All,
I have a doubt regarding the calculation of number of contacts
between two
groups. Because, I am getting different number of contacts
calculated
through g_hbond -contact option and g_mindist -on option.
I have used same cutoff for distance (0.6nm) in both the cases.
How different are the results? The g_hbond code is very complex, but
you'd probably have to go into the inner workings of both programs to
understand why. I also do not know whether other settings in
g_hbond will
matter, like -merge, or whether or not g_hbond will only calculate
contacts
among H-bond participating groups.
-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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
==============================**==========
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users
>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists
>
--
*-----------------------
Thanks and Regards,
Bipin Singh*
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
