[gmx-users] "freezegrps" concept

[Sarath Chandra Dantu]

On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA <yuvrajthedon at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101215/663eacb6/attachment.html>