AMBER Archive (2006)

Subject: Re: AMBER: Unit of force

From: Adrian Roitberg (
Date: Wed Nov 08 2006 - 06:57:00 CST

Kakali Sen wrote:
> Dear all,
> We have modified amber code to apply constatnt stretching on DNA by
> applying an external force.
> When we apply force in units of kcal/mol/ang we get a force extension curve
> which looks very similar to the experiment one but the force scale is in
> between 100-2000 pN rather than between 10-100 pN as in experiment. It
> is an order higher.
> On the other hand if we say that force is in pN in amber force array
> then we have the correct force extension plot (that is between 10 to 100
> pN) but then we have problem in getting the correct stretch modulus.It
> of one order lesser
> than that obtained experimentally.
> Thanks for your patience and looking forward for suggestions.
> Kakali.

Two or three important things about this:

First, are you sure you have the exact same setup as the experiment ? I
mean solvent, etc ?

Second, the rate at which you pull is CRUCIAL. I bet that you are
pulling orders of magnitude faster than experiment. There is not much
you can do about this, but you should at least do it a number of times
frm different initial snapshots and different pulling rates to see what
the fluctuations are.

Third. There is code in amber 9, under the flag "jar" to perform
constant velocity pullings. We are coding constant force now and might
be available for the public later on.


                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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