Hi Zhenlong, I guess that some molecules got split over the boundaries during equilibration. You have to make them whole before changing the box. Better to start off with a rhombic dodecahedron though.
Cheers, Tsjerk On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li <[email protected]> wrote: > Dear all, > My system is based on Martini, needs a dodehedron box. > Initially, it was minimized and equilibrated with a cubic box smoothly. Then > I used the follow command to > translate the box in to dodehedron: > editconf -f f0.gro -bt dodecahedron -d 2 -o vesdode.gro > But with this change, the simulation always blows up with the message below. > > Since those atoms are most at the boundary of the box, I think it is because > the overlap of boundary atoms > with the new box type. I tried different value for -d and -box, but still > have the same problem. > > Can anybody give me any hint to fix this? > > Thanks a lot! > Zhenlong > > --------------------------------------------------------------------------------------------------------------------------------- > Making 3D domain decomposition 7 x 4 x 3 > > A list of missing interactions: > Bond of 79872 missing 7 > G96Angle of 50688 missing 9 > > Molecule type 'DPPC' > the first 10 missing interactions, except for exclusions: > G96Angle atoms 6 7 8 global 37638 37639 37640 > Bond atoms 7 8 global 37639 37640 > G96Angle atoms 10 11 12 global 37642 37643 37644 > Bond atoms 11 12 global 37643 37644 > > Molecule type 'DUPC' > the first 10 missing interactions, except for exclusions: > G96Angle atoms 10 11 12 global 38446 38447 38448 > Bond atoms 11 12 global 38447 38448 > > Molecule type 'DPPC' > the first 10 missing interactions, except for exclusions: > G96Angle atoms 3 5 6 global 43395 43397 43398 > Bond atoms 5 6 global 43397 43398 > G96Angle atoms 5 6 7 global 43397 43398 43399 > > Molecule type 'DUPC' > the first 10 missing interactions, except for exclusions: > G96Angle atoms 6 7 8 global 45330 45331 45332 > Bond atoms 7 8 global 45331 45332 > > Molecule type 'DUPC' > the first 10 missing interactions, except for exclusions: > G96Angle atoms 5 6 7 global 57173 57174 57175 > Bond atoms 6 7 global 57174 57175 > G96Angle atoms 6 7 8 global 57174 57175 57176 > > Molecule type 'DPPC' > the first 10 missing interactions, except for exclusions: > G96Angle atoms 6 7 8 global 63822 63823 63824 > Bond atoms 7 8 global 63823 63824 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
