On 9/9/17 1:50 AM, ISHRAT JAHAN wrote:
Dear all, I have done 100ns md simulation of protein with drug using amber99sb.ff with gromacs-5.1.4 version. After simulation i found my protein broken into smaller parts in .gro file but when i load the final xtc file to pr.gro molecule does not break. I have applied -pbc nojump ,cluster and whole but unable to solve the problem. Will anyone help me to solve the above problem.
We'll need to see your commands, exactly as issued, to be able to say anything. In general:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
