VMD-L Mailing List
From: Nicola Giacche' (nicolag_at_chimfarm.unipg.it)
Date: Tue May 24 2011 - 09:42:19 CDT
- Next message: Ajasja LjubetiÄ: "Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0"
- Previous message: maria goranovic: "trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0"
- Maybe in reply to: Olaf Lenz: "Re: pbc unwrap not complete"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi,
the big "jumps" were due to "glue" feature of Desmond. Indeed in my
specific system, where there were not "solvent" but only "solute"
molecules (including the custom solvent), caused such a problem.
Turning off the "glue" feature, as recommended by James Watney of the
Desmond-User Group, the simulation runs smooth without jumps.
Nicola
Il 23/05/2011 17:20, Olaf Lenz ha scritto:
> Hi!
>
> The reason why "pbc unwrap" can not work correctly is simply that the
> atoms move to far between the different frames. If you look at "resid
> 40", you'll notice that in the very first step the molecule moves almost
> half of a simulation box length. In fact, some of the atoms move even
> further. As a consequence, these atoms are wrapped, so that they are
> very far from the other atoms in the same residue.
>
> I don't see a simple way to solve this using the pbctools at the moment.
> One could probably modify the pbctools such that it somehow takes into
> account both the step size (unwrap), the box size (wrap) AND the
> molecular bonds (join), but so far it does only one of it at a time.
>
> I think the only way to circumvent this is to record more frames in the
> trajectory and to make sure that no atom moves further than half a box
> length between too consecutive frames.
>
> Olaf
>
-- Nicola Giacchè, PhD. Dipartimento di Chimica e Tecnologia del Farmaco. Faculty of Pharmacy, University of Perugia via del Liceo 1, 06123 Perugia (Italy) Tel +39 075 585 5169 E-mail: nicolag_at_chimfarm.unipg.it
- Next message: Ajasja LjubetiÄ: "Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0"
- Previous message: maria goranovic: "trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0"
- Maybe in reply to: Olaf Lenz: "Re: pbc unwrap not complete"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]