AMBER Archive (2007)

Subject: AMBER: Box dimensions

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Feb 16 2007 - 09:13:45 CST

Hello Amber

I have a question about the periodic box dimensions. When I initially
run my protein in a water box, I run at constant pressure and then after
I get to a density of 1g/l I run at constant volume. My question
involves the "shrinkage" in the box dimensions during my constant
pressure run. My box size went from 64 x 64 x 84 to 59 x 59 x 78.
Someone made a comment to me about how this size of change is not
usually expected. What is the effect on my production MD run due to this
effect?

 

Thanks Steve

 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu