Thanks for the reply Dr. Trayder and Dr. Justin. I have performed unrestrained MD with a ligand bound protein having surface exposed binding pocket (link of the image attached for clarification). I have used a cubic box with vectors 6.432nm and the system size was 4.117 3.878 and 4.059 (in nm).
http://researchweb.iiit.ac.in/~bipin.singh/snapshot.png My doubt is how to discriminate between a real ligand binding/unbinding process and the rebinding observed due to PBC effects (i.e. when ligand diffuses out the box and a subsequent another ligand comes and bind from the adjacent periodic image, which may seen as a rebinding event during distance calculation). On Tue, Oct 8, 2013 at 6:37 AM, Trayder Thomas <trayder.tho...@monash.edu>wrote: > With a ligand diffusing as freely as I'm assuming (you've omitted a lot of > info, box size etc.) you aren't going to get PBC to play nice, although > -nojump should have atleast given you a different wrong answer. > > Centering the system on the same point you are using to define the binding > pocket (may require custom index groups) should get you something more > reasonable looking. > > Also, it depends on the size of your protein and what you're doing but you > should consider if it's even relevant whether the ligand is 2nm away or 5? > > -Trayder > > > > On Tue, Oct 8, 2013 at 6:53 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 10/7/13 1:39 PM, bipin singh wrote: > > > >> Thanks for the reply Dr. Justin. > >> I have also thinking of the same possibility but to further confirm, I > am > >> sending the link for the plot of the distance between the COM of ligand > >> binding pocket and COM of ligand molecule, please find some time to > have a > >> look at the plot and let me know if it seems a feasible behaviour > during a > >> simulation. > >> > >> http://researchweb.iiit.ac.in/**~bipin.singh/plot.png< > http://researchweb.iiit.ac.in/~bipin.singh/plot.png> > >> > >> > > Looks like nothing more than random motion to me. Since you haven't told > > us what you're doing (unrestrained MD? pulling?), it's hard to comment > > further. > > > > -Justin > > > > > > On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> > >> > >>> > >>> On 10/7/13 10:46 AM, bipin singh wrote: > >>> > >>> Hello All, > >>>> > >>>> I have calculated the distance between the binding pocket of protein > and > >>>> the ligand molecule but due to ligand diffusion out of box, I am > getting > >>>> wrong distance as first it increases till 5nm and then decrease again > to > >>>> around 1nm during the simulation (which is not possible). > >>>> > >>>> I have fitted my trajectory with using trjconv -pbc mol -ur compact > >>>> -center > >>>> (protein) option. > >>>> > >>>> I have also tried the -nojump option but getting the same results for > >>>> distances. > >>>> > >>>> Please suggest how to get the real distance without the PBC effect. > >>>> > >>>> > >>>> It sounds like that very well could be the real distance. If the > >>> ligand > >>> diffused out, it simply becomes part of the solvent around the protein > >>> and > >>> can diffuse around freely. > >>> > >>> -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 > -- *----------------------- 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
