Dear Justin, I would like to correct myself. Actually, the COM of the two groups - Protein and Ligand are about 5 nm away at the end of the pulling process. But the rear end of the ligand is just 0.6 nm away from the closest Amino acid of the Protein. Is that reasonable for the Binding affinity calculations?
Best Regards, Bhagyesh ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Friday, June 2, 2017 4:10:21 PM Subject: Re: [gmx-users] Doubt about gmx wham analysis On 6/1/17 6:29 PM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > Since I have the settings pull_coord1_dim = Y Y Y, I am not sure which axis > the ligand is pulled. My initial simulation box size was 5 nm in each side. > To care of the pulling of the ligand in any direction I made the box size 14 > in each direction filled with water. The simulation runs perfectly and ending > with the ligand almost 0.6 nm away from protein. But all this takes lot of > computation power due to the need for rigorous sampling. Is there any way to > cut the computation cost while maintaining the accuracy? > 0.6 nm is not very far, especially if your solute-box distance is 14 nm (which would be appropriate to get a full dissociation). There's not much to do aside from making sure you're using an efficient box, e.g. rhombic dodecahedron. A cube is inefficient. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
