I have created my files long time ago using version 4.0.7. But now analyzing the same files using g_hbond/g_mindist using version 4.5.5
On Sun, Sep 1, 2013 at 10:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/1/13 1:17 PM, Nidhi Katyal wrote: > >> 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. >> >> > What version of Gromacs are you using? > > -Justin > > >> >> 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 >>>>> <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> >>>>> > >>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> >>>>> >>>>> Mailing_Lists/Search<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> >>>>> <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> >>>>> <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 <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? 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