On 4/25/19 7:10 AM, SUSHMITA BASU wrote:
Dear users, I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. I understand why for a pull of 5nm, the z axis of the box is set at 12 nm, but did not get how the x and y axis of the box is determined. This question might be very basic, but I cannot figure out how to do it. Kindly help me in this. Thanks in advance.
I built a standard box with editconf -d and then used the x and y box vectors and extended along z.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
