From: Albers, Thomas (TALBERS_at_augusta.edu)
Date: Thu Aug 03 2017 - 12:48:24 CDT
Hello!
I would like to explore the energy profile of the conformational change in a turn in my protein. The Ramachandran angle phi varies from 50 to 260 degrees in that system; the range between -100 and 50 degrees is not visited.
The interval for dihedral angles in NAMD is -180 - 180 degrees. How to get around the periodicity issue, because as far as I can see the interval beyond 180 deg, where the angle wraps around, is not reached. Here is an excerpt from the .count file:
..
172.5 15805
177.5 13467
182.5 0
187.5 0
..
The colvar is defined like this:
colvar {
name phi265
width 5.0
lowerboundary 50
upperboundary 260
lowerWallConstant 0.2
upperWallConstant 0.2
dihedral {
group1 { atomNumbers 4365 }
group2 { atomNumbers 4367 }
group3 { atomNumbers 4369 }
group4 { atomNumbers 4372 }
}
}
abf {
colvars phi265
}
How to get around the wraparound issue?
Thanks,
Thomas
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