questions regarding output data of an ABF simulation

From: Anahita Tafvizi (atafvizi_at_fas.harvard.edu)
Date: Mon Aug 07 2006 - 15:27:34 CDT

Dear fellow NAMDers,
I'm seeking your help regarding a PMF calculation in NAMD using ABF.

I am trying to run ABF for lacI protein sliding along the DNA. I define my
abf1 and abf2 as the last pair of DNA and the protein respectively. the last
pair of DNA is completely fixed (occupancy= 100.0), and the backbone of the
rest of the DNA is also fixed but with a smaller occupancy (5.0). The
protein is moving toward the last pair as I want, but I don't have any
useful output data. I mean I can see the movie, but I my history file is
just containing zeros.

I've attached my namd file.

Thanks a lot in advance for your replies.

Best regards,
Anahita


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