hi dear justin A few months ago I asked you a question about LIE method. According to your guide, i wrote a new .mdp file that didn't use PME (I used RF) and used following command for protein-ligand complex and ligand-sol simulations: mdrun -s newtpr.tpr -rerun full20ns.xtc then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command. But the obtained free energy has great difference with the experimental value.
You told me that i must re-calculate energies from PME systems, then i must take the difference of the energies from another system where the same correction hasn't been applied. Please explain this. How do I do it? I have urgent need to calculate the free energy. Thank you sincerely On Monday, January 13, 2014 5:22 AM, Justin Lemkul <[email protected]> wrote: On 1/12/14, 5:18 PM, Mahboobeh Eslami wrote: > dear Justin thanks a lot > I use Amber03 force field and TIP3P water model for my system. following > options > are used in first my mdp file: > nstlist = 5 > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > I have following questions. if possible, please answer them. > 1) are these options good for LIE method? do LIE method need especial options? Run settings like these are dependent upon the force field. LIE is simply a post-processing technique. > 2) I saw following advice in gmx forum " save a lot of frames to get > reasonably > accurate numbers " (http://gromacs.5086.x6.nabble.com/PME-td4450969.html) > do you have especial comment for frame saving? No insight there. I am not familiar with the details of what was proposed in that post. As far as I know, most people do not attempt to re-figure energies like that; they simply re-process using RF or long cutoffs (RF is better). > 3) I use *coulombtype = *cutoff and rcoulomb = 1.0 in new mdp file for > rerun energies. are these options good or not? No, plain cutoffs are very inaccurate. -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 [email protected] | (410) 706-7441 ================================================== -- 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 [email protected]. -- 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 [email protected].
