Hi,
I am a newbie in amber after few years of using GROMACS. In the GROMOS force-field, nonbonded interactions are treated using a twin-range cut-off scheme: interactions within the 0.8 nm are calculated every step whereas interactions within 1.4 nm are update every 10ps. This is true for both VDW and electrostatic interactions, when Reaction-Filed is being used.
I have search the literature to see what is being used with amber, and found variations between 0.8 (cut = 8) to 1.4 nm for the cut-off.
Assuming I am simulating a proteins/water system using ff12 and PME (for the electrostatic calculations), what should be the parameters, and how I define them.
Also, it will be great if someone now a guide or a tutorial specifically written for GROMACS users moving to amber. Or maybe a 'translation' of the flags used in GROMACS to amber.
All the best,
Itamar
--
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass.monash.edu
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Received on Sun Nov 25 2012 - 19:00:01 PST
