AMBER Archive (2008)

Subject: Re: AMBER: SMD-related questions

From: Jackie. J. Shen (shj.ecust_at_163.com)
Date: Tue Dec 30 2008 - 20:27:16 CST

Hi all,

In my opinion, the unit of force in AMBER SMD is Kcal mol-1 A-2, which is the same as Restraint_WT. The translation is as follow:

1 Kcal mol-1 A-2 = 418.4 KJ mol-1 nm-2 ~=69.5 pN A-1

The velocity of SMD in AMBER was set through distance and time. If the stiff spring constant was used, the velocity is nearly constant.

In amber, a stiff spring constant is recommended for the Jarzynski equility. Dodson has provided some very useful referecens. Thanks to him.

Anyone could correct if I made mistakes.
                 
Jackie. J. Shen
2008-12-31

-----------------------Original-------------------------
>From£ºAlessandro Nascimento
>Sent£º2008-12-29 21:09:52
>To£ºamber_at_scripps.edu
>Cc£º
>Subject£ºAMBER: SMD-related questions

>>
>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?
>
>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?
>
>Could someone also provide some references (or share personal
>experiences) regarding the spring constant on SMD simulations
>(especially in Amber FF)?
>
>Thanks a lot in advance and a happy new year for all,
>
>--alessandro
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