Even after giving same cutoff radius of 0.35nm in both, I am getting around 400 contacts per timeframe with mindist but 0 contacts with g_hbond.
On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/1/13 1:08 PM, Nidhi Katyal wrote: > >> The two groups are: protein and cosolvent molecules. With g_mindist -on , >> I am getting values of around 6500 per timeframe. But then why g_hbond >> giving different results. >> >> > Are you using the same cutoff radius for both? > > -Justin > > >> On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/1/13 12:50 PM, Nidhi Katyal wrote: >>> >>> Hello, >>>> I would like to calculate number of contacts between two groups, for >>>> which >>>> I am using following command: >>>> g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 50000 >>>> I am getting 0 as the output. But when I am calculating number of >>>> hydrogen >>>> bonds between the same two groups by using the above command without >>>> contact option I am getting 5.2 as the output. >>>> My question is wouldn't number of contacts be higher than number of >>>> hydrogen bonds since hydrogen bonds are subset of contacts. >>>> >>>> >>> In theory, but something might be failing. What are the groups you are >>> choosing? What is your expected outcome? What does the output of >>> g_mindist -on give you? >>> >>> -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@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | >>> (410) 706-7441 >>> >>> ==============================****==================== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**==================== > > 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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > 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> > -- 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
