MDFF volumetric map

From: Ivana (stankoviciv_at_gmail.com)
Date: Wed Feb 27 2013 - 11:43:03 CST

Hello, everybody!

I have questions about a volumetric map in MDFF.

1-What is the format .dx, the 3 columns?

# Data from VMD
# created by volutil, T = -1.00 Kelvin,
object 1 class gridpositions counts 126 76 63
origin -10 -41 -25
delta 1 0 0
delta 0 1 0
delta 0 0 1
object 2 class gridconnections counts 126 76 63
object 3 class array type double rank 0 items 603288 data follows
1 1 1
1 1 1
1 1 1
1 1 1
1 0.998984 0.916842
0.903898 0.891292 0.835943
0.719295 0.718527 0.718508
.........

2-What is the function of a volumetric map's box?
3-Why does the entire target map (with the box) have to be within the water
box?
4-Is there a way to calculate a volume of .dx or number of atoms inside the
.dx?
5-What is the difference between volumetric map and trimmed volumetric map
in the density values?
6-I don't understand the formula for potential energy V=(1- /max )
for >0;
V= for =0 Does it mean that the force is higher in low density regions
and decreases with increasing ? Units of ?
http://www.ks.uiuc.edu/Research/mdff/method.html
7-Where is in .dx file, in what units?

Only 1- would help me a lot, thank you!
Ivana Stankovic, State University of Campinas, Brazil

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