On 2/9/15 8:55 PM, Agnivo Gosai wrote:
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.
If you're using the pull code, yes you are. There's a force constant associated with the spring that is applying the umbrella (harmonic) potential. If that's not clear, stop everything you're doing and read every paper and book chapter you can find so you understand what you're doing rather than just typing in what a tutorial said.
Could any user suggest any source / literature for choosing "restraint forces" for DNA/protein systems ?
There is a wealth of information on umbrella sampling, steered MD, etc. Google will show you in seconds.
Regarding window setup, is it the spacing of the windows ?
Possibly.
Except for simulation time is there any other method for increasing sampling ?
Time is the primary issue here (as in most any simulation). -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.
