AMBER Archive (2007)

Subject: Re: AMBER: umbrella sampling dihedral restraint question

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 18 2007 - 00:46:16 CDT

On Thu, Jun 14, 2007, Cen Gao wrote:

> 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."

The dihedral restraint code knows about periodicity, so you are not restricted
to the 0 to 360 range.
>
> if r2=r3=10 degree, do we still set r1=0 and r4 =360?

If you set r1 to -50 and r4 to 70, then you would have a parabolic region
of 60 degrees on both sides of 10 degrees.

> Set r1 = r2-180 and r4= r3+180? for 10 degree, we need to
> set r1= -170 and r4=190?

You should check, but I think the above is correct.

>
> 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,

You have to use trial and error. Generally, for umbrella sampling, you want
overlap between adjacent windows, so the restraint has to be weak enough to
allow you to obtain the required breadth. There is (unfortunatly) no magic
number that always works, but a little experience will usually help. Don't
be afraid to experiment.

...regards...dac

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