[gmx-users] Average number of salt bridge

[bharat gupta]

Thank you Justin... that's what I was looking for ...


On Tue, Nov 19, 2013 at 2:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/14/13 10:18 PM, bharat gupta wrote:
>
>> Hi,
>>
>> How can I calculate the average number of salt bridges between two
>> residues
>> during the entire simulation ??...
>>
>>
> Unless you've got some wildly noncanonical residues, this is a binary
> function.  Either the salt bridge exists (1) or does not (0).  You can
> define a salt bridge a number of ways, but the easiest and most common is
> the distance between the COM of the positive and negative moieties.  Use
> g_dist over time and post-process the output to determine the fraction of
> time spent within the distance cutoff; it's a much more useful quantity.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
> --
> gromacs.org_gmx-users mailing list    gromacs.org_gmx-users@
> maillist.sys.kth.se
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_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
>