[gmx-users] cutting a trajectory and continuing from a part of it

[Justin A. Lemkul]

Sajad Ahrari wrote:
> Dear users
> is there any way I can omit a part of my run and continue again from 
> there on? in fact my protein escaped the box i had introduced to it, 
> after 13ns past. I am searching for a way to bring it back and continue 
>  my run after 13th ns.
> I do appreciate your kind help.

There is no need to do this.  Such behavior is a normal consequence of periodic 
boundary conditions.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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