[AMBER] undo iwrap wrapping

From: Paul Brandt <brandt.j.gene.com>
Date: Mon, 5 Apr 2010 00:21:22 -0700



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?




AMBER mailing list
Received on Mon Apr 05 2010 - 00:30:03 PDT
Custom Search