Re: [AMBER] unusual structure after heating. why?

From: Jason Swails <>
Date: Thu, 15 Jan 2015 07:42:29 -0500

On Thu, 2015-01-15 at 12:19 +0330, Atila Petrosian wrote:
> Dear amber users

> After heating, when I saw heat.mdcrd file using VMD, unfortunately, I
> encountered with unusual structure (please note the figure in the following
> link: (
> What is the reason of this issue?

This is caused by loading the mdcrd file as an "Amber Coordinates"
instead of "Amber Coordinates with box".

See the discussion in the 2nd basic tutorial (on VMD):

> I am beginner in amber, please help me to resolve this problem.

Then I will make another suggestion. Set the input variable "ioutfm=1"
in the &cntrl section of the sander/pmemd input file. This will cause
the trajectories to be written in "NetCDF" format. These files are
better than ASCII trajectories in almost every way:

1. They are smaller than ASCII trajectories and take up less space
2. They store coordinates with much higher precision
3. They read (and write) MUCH faster
4. They are more fault-tolerant if a frame is corrupted
5. They are extensible

So there is only one "Amber NetCDF trajectory" format in VMD (since it
is easy to determine whether box information is present or not without
needing to tell VMD so).

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 15 2015 - 05:00:03 PST
Custom Search