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On 9/13/15 11:35 PM, Idriz Seferi wrote:
Hi all, I have a question regarding Umbrella Sampling in gromacs 5.1. I am following the tutorial of Dr. Lemkul () and I am getting errors about the parameters when I am running gmx grompp. Specifically, I am constantly getting an error on the pull-rate option. Dr. Lemkul uses the following options for the pull code: ; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = Chain_A pull_group2_name = Chain_B pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 However, when I run gmx grompp with these parameters I get a warning on pull_start, pull_rate1, and pull_k1. With the help of the gromacs webpage on mdp options, I modified the above list to the following: pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = Chain_A pull_group2_name = Chain_B pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_coord1_rate = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
These modifications look correct to me. I have fixed them in the tutorial (sorry for the typos; working too quickly). What is the specific error grompp raises when using these (copied and pasted, please)?
-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.
