Hi .. You didn't mentioned the box-type by -bt flag You mention that...I hope your problem will be resolved.
On Thu 22 Aug, 2019, 7:24 PM sunyeping, <sunyep...@aliyun.com> wrote: > 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. > > 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. > -- 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.
