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 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 <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> > -- *----------------------- 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
