Thanks, Tsjerk. Exactly as what you said, it was because split of molecules over the boundary. It runs smoothly right now as I started with a dodecahedron box.
best, Zhenlong On Thu, Oct 6, 2011 at 12:24 PM, Tsjerk Wassenaar <[email protected]> wrote: > 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 >
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