Dear Users Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating the topology and the itp files. Therein , automatic position restraints are generated. Now, I have never used manual restrain force constants.
Could any user suggest any source / literature for choosing "restraint forces" for DNA/protein systems ? Regarding window setup, is it the spacing of the windows ? Except for simulation time is there any other method for increasing sampling ? I have read the manual but could not find anything. I am searching in the web also. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. On 2/9/15 4:11 PM, Agnivo Gosai wrote: > Dear Users > > My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's > tutorial advocates a 10 ns simulation time. I found that after running WHAM > , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my > histograms have two peaks!! > So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100 > ps NPT equilibration and then a 1 ns umbrella sampling in each of my > windows. The generated PMF curve is also not smooth and is discontinuous at > one position which I think I can fix by adding more windows around that > co-ordinate. > > A picture is linked : > HISTO > < > https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web > > > > Kindly help. > > You need to assess convergence like you would for any type of system. Most of your peaks look rocky, so that generally indicates insufficient sampling, poor window setup, suboptimal restraint force constant, or some combination of those. Don't think that 10 ns is some magic number, either. It worked for that system after I did a bunch of checking and the result was converged. Some umbrella sampling takes way more time. -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.