AMBER Archive (2004)

Subject: AMBER: ptraj projections help

From: Thomas C. Bishop (
Date: Mon Apr 19 2004 - 12:41:08 CDT

Dear amber,

 I have a couple of questions about ptraj.

1) Can the modes be read from a stack instead of disk
to avoid an additional "sweep" through the trajectory as stated
in the Amber 8 manual pg 210.

2)How does one construct an animation of different normal modes
given the output data?

3) Does anyone have a script they want to share that does 2)?

4) Any recommended references for more information??

Of interest may be the Amber Archive on Quasi-Harmonic/PCA and refs therein.


Center for Bioenvironmental Research Tulane and Xavier Universities 1430 Tulane Avenue SL-3 New Orleans, LA 70112 Phone: 504-988-6203 Fax: 504-585-6428 ----------------------------------------- Alternate Contact: Center for Computational Sciences Voice: (504) 862-8391 -----------------------------------------

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