AMBER Archive (2009)

Subject: Re: AMBER: SMD-related questions

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Jan 02 2009 - 07:21:53 CST

On Mon, Dec 29, 2008 at 8:07 AM, Alessandro Nascimento wrote:
> Hi guys,
> I have been through the manual but could not find the units of force
> for SMD. I assume it is pN as in NAMD. Is that correct?

No. As Jackie pointed out, units of force in Amber are kcal/(mol A**2).

> A second question is: the steering velocity is not set, as in NAMD, in
> the simulation input file. I presume it is given by the steering
> distance over the simulation time (r2a/nstlim). Is that correct?

That is correct.

> Could someone also provide some references (or share personal
> experiences) regarding the spring constant on SMD simulations
> (especially in Amber FF)?

Besides the references you've already got from Dodson, I'd recommend
that you take a look at the following ones, that specifically use
Amber:

[1] Torras, J., G. d. M. Seabra, et al. "A Multiscale Treatment of
Angeli's Salt Decomposition." Journal of Chemical Theory and
Computation (http://pubs.acs.org/doi/abs/10.1021/ct800236d)

[2] Xiong, H., A. Crespo, et al. (2006). "Free Energy Calculations
with Non-Equilibrium Methods: Applications of the Jarzynski
Relationship." Theoretical Chemistry Accounts: Theory, Computation,
and Modeling (Theoretica Chimica Acta) 116(1 - 3): 338-346.

[3] Roitberg, A. E. (2005). "Nonequilibrium approaches to free-energy
calculations." Annual Reports in Computational Chemistry 1(1):
103-111.

[4] Crespo, A., M. A. Marti, et al. (2005). "Multiple-Steering QM-MM
Calculation of the Free Energy Profile in Chorismate Mutase." J. Am.
Chem. Soc. 127(19): 6940-6941.

Good luck,
Gustavo.
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