AMBER: umbrella sampling dihedral restraint question

From: Cen Gao <>
Date: Thu, 14 Jun 2007 16:33:51 -0400

Hi all:
I am currently running umbrella sampling for a 2D psi/phi dihedral
map. My restraint is like:
since dihedrals are periodic, there is one sentence in the manual
bothers me a little bit. It said " The values r1 and r4 should be far
away from 170(the manual uses 170 as minimum), so that the potential
is essentially harmonic every where."

My concern is do I need to use a different r1 and r4 for different
simulation window, especially when r2 and r3 near 0 or 360 degree. Say
if r2=r3=10 degree, do we still set r1=0 and r4 =360? If that is true,
when r =350, the k(r-r2)^2 is very large, while actually it is
supposed to have a similar energy as r= 30,since the potential is
symmetric and 30 and 350 degree are all 20 degrees from the minimum.
Or we might need to distribute the r1 and r4 evenly beside the
minimum. Set r1 = r2-180 and r4= r3+180? for 10 degree, we need to
set r1= -170 and r4=190?

Another question is when I set the force constant too high, the
simulation just blown out. (log file said vlimit exceeded for step
***.) Is that a normal error for too high spring constant? How to
check whether I get a reasonable constant, just make sure it doesn't
blow out and also see the angle distributed evenly around the minimum
from the MD trajectory? Thanks

I am new to amber and this is my first post. Any suggestion will be
highly appreciated.
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Received on Sun Jun 17 2007 - 06:07:25 PDT
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