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? Best regards, Ali
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of Justin Lemkul Sent: dinsdag 15 januari 2019 15:01 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] regarding editconf On 1/15/19 7:46 AM, Ali Khodayari wrote: > Dear users, > > > > I am trying to reorient and re-center my solute using editconf. > Performing such I can place the structure at the desired place, yet it > is outside the box when I visualize it in VMD. It leads to an error > after mdrun complaining about a water molecule not being settled. > > Here is the command I use: > > $ gmx editconf -f cell.gro -o cell_newbox.gro -princ -bt triclinic -c > -center 0 0 0 -rotate 0 350 0 -n ndx.ndx > > Do you see where the problem is? First, there is no such thing as "outside" an infinite box, so that should not be the cause of any actual problem. Regarding editconf, you're doing too many things at once, which may be mutually exclusive, so you may not be getting what you want. You're telling editconf to align the longest axis along x (with -princ) but also to rotate about y (-rotate 0 350 0). Don't do both of those at once. -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. -- 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.