On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA <yuvrajthe...@gmail.com>wrote:
> Hello > > I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic" > as box with distance of 1nm b/w solute n box. > Protein is going out of the box after equilibration step. Any solution? > > The protein does not diffuse out of the box. Use for eg: trjconv -pbc nojump on your trajectory. For more information refer to the link below... http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Best Wishes, Sarath > Should i use *freezegrps* option to restrict protein movement. Please > provide some light to this option. What effect it will have on the whole > system? > > -- > Yuvraj > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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