On 1/15/19 9:34 AM, Ali Khodayari wrote:
Thank you for your response Justin! I don't really see how it can cause an error, while it might be just a visualization defect in VMD. Previously, I tried to perform each step separately, like doing a centering by -center 0 0 0, but even performing this step leads to the error "step 0: Water molecule starting at atom 40225 can not be settled." The only difference would be a change in the coordinates, no? It is not due to the fact that I am using 5.1.2 version, is it?
Systems can become unstable for any number of reasons, but not simply because some part of a protein appears to be protruding into space. That's just normal PBC.
5.1.2 is very old but I don't know of any specific reason why it should cause a problem.
-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.
