> > Message: 3 > Date: Thu, 22 Aug 2019 21:53:25 +0800 > From: "sunyeping" <sunyep...@aliyun.com> > To: "gromacs.org_gmx-users" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] How to make all parts of a protein in the > periodic box in when running "gmx editconf" command > Message-ID: > <0c07c92c-a134-4057-a8a2-13a1143ae486.sunyep...@aliyun.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > I run the"gmx editconf" command to make a periodic cubic box around my > protein for adding water: > > gmx editconf -f protein.gro -o newbox.gro -c -d 1.0 > > Then I visualize the priodic box in VMD. I find that one end of my protein > is out of the box (Please see the part in red circle in image at > https://drive.google.com/file/d/1M6msh1UA0fOZ4GOuGJVlJHTOtHrzwh7u/view?usp=sharing). > Even if I increase the value of "-d" option to 1.5, this end of the > protein is still out of the box. This will result in visualization problem > of the MD trajectory. This part at one end of the molecule which is out of > the box will jump to the other end of the molecule in VMD and pymol. Please > see the part in the red circle in the image at ( > https://drive.google.com/file/d/1GAP4oS78nAB6p-ZhPmT9A-6ZZnohhkeq/view?usp=sharing). > The is the image for em.gro the structure after energy minimization. The > trjconv command with -pbc cluster -center -ur cpmpact command cannot solve > the problem. > > Have you tired the -pbc nojump flag see if that can give you a different representation of the structure?
Shi > So could you tell me how to keep all part of the protein in the periodic > box when running "gmx editconf" command? Thank you in advance. > > Yeping > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 184, Issue 58 > ****************************************************** > -- 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.
