AMBER Archive (2002)

Subject: Amber Trajectories + VMD (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Tue Dec 03 2002 - 16:58:00 CST

---------- Forwarded message ----------
Date: Tue, 03 Dec 2002 14:44:41 -0600 (CST)
From: joelkp_at_erc.msstate.edu
To: Amber Mailing List <amber_at_heimdal.compchem.ucsf.edu>
Subject: Amber Trajectories + VMD

I'm trying to make an animation in VMD from the trajectory created by an Amber 7
molecular dynamics run. Here's my input file:

----------
Initial dynamics w/o restraints - AChE / CYX / HID / Solvent / Neutral
 &cntrl
   ntwx = 10,
   ntf = 2, ntb = 2,
   nstlim = 100,
   ntp = 1,
   ntc = 2,
   tempi = 300.0, ntt = 1,
   lastrst = 3000000,
 &end
----------

As you can see, there's only 100 steps, and the coordinates get written out
every 10 steps, indicating that this should be a 10-frame animation. I open up
VMD 1.7.1, click on 'Molecule', then 'Load From Files', select 'parm and crd',
and choose my input parameter file and my trajectory file. When I press 'Load
Molecule', VMD proceeds to read in the files, showing a rapidly-increasing
'frames' count. The problem is that this 'frames' count continues to increase
indefinitely, when it should logically stop at 10. The 'atoms' count also
remains at 0.

Are there any format-conversion steps I should be taking that I'm not? Or is
this not the correct procedure?

-Joel