Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time

From: case <>
Date: Mon, 10 Jan 2011 09:05:50 -0500

On Mon, Jan 10, 2011, xueqin pang wrote:
> I am using Amber11 for MD simulation. It works nice but when
> run a segment for 20ns ( that is 5000 snapshots) at a time, I got
> problem with the last several snapshots in the output dcd file. Taking
> the rmsd of the protein backbone for example it is about 230A while

You need to say exactly how you computed the rmsd. This is probably a simple
matter of making sure you are correctly reading the box information from the
trajectory file, but without even know what program you are using (much less
what input) we can't help much.


AMBER mailing list
Received on Mon Jan 10 2011 - 06:30:04 PST
Custom Search