you can't undo wrapping, since there is no way to know which of the infinite
lattice of cells the molecule was in. for your case, though, you just need
to use the ptraj "center" and "image" commands. search the archives and look
in the manual, there is plenty of info on it.
the basic idea is to center on 1 strand, then image the system. you can then
center on both and image again if you want the water or other things to
surround the dimer. it's impossible to give a sample command since you need
to make it correct for your system.
On Mon, Apr 5, 2010 at 3:21 AM, Paul Brandt <brandt.j.gene.com> wrote:
> Hello,
>
>
>
> Is there a tool to unwrap the wrapping done by pmemd and sander? I ran
> into
> trouble with simulations that required backtracking and setting iwrap=1 to
> continue. Since then I started using it for all my simulations from the
> start. This was a mistake. I'm seeing a situation analogous to splitting
> of double strand of DNA.
>
>
>
> I've seen the discussions on the mail reflector regarding the need to
> re-implement binary output and leave wrapping for post-processing. This
> would be nice. Has this been implemented?
>
>
>
> Can I unfold an improperly imaged trajectory? Should I only set iwrap=1
> when it is needed?
>
>
>
> Thanks,
>
> Paul
>
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Received on Mon Apr 05 2010 - 04:00:02 PDT
