On 10/30/14 1:19 AM, Sathish Kumar wrote:
Dear gromacs-users, I have run the umbrella sampling with the help of tutorial of justin. In my system rna is binding with gold nanoparticle. To find out the binding energy, i run the umbrella sampling using the space 0.1 nm and i got total 79 configurations, each configuration was run for 5 ns. Out of the 79 configurations, only for the 78 and 79 configurations while running mdrun i am getting the following error. Fatal error: Distance of pull group 1 (12.277075 nm) is larger than 0.49 times the box size (12.526427) I have used pull geometry = distance How can i solve this problem, please help me in this regard.
As described in the tutorial, the pulled distance (when using geometry = distance) cannot exceed half of the box size due to issues related to periodicity of the system. You'll have to decide whether or not you need to be pulling this far, but if you do, you need to set up a larger box.
-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.