Dear Amber users
I am trying to use GB/SA model to calculate the internal energy of my DNA molecule by stripping water molecules from the solvated trajectory. But I do not know the updated GB/SA methodology. And I checked the references in Amber16 manual and it refers to the following:
Tsui, V.; Case, D. Molecular dynamics simulations of nucleic acids using a generalized Born solvation model. J. Am. Chem. Soc., 2000, 122, 2489–2498
Tsui, V.; Case, D. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers (Nucl. Acid. Sci.), 2001, 56, 275–291
I would really appreciate if one can give me guidance on updated GB/SA methodology( if there is any) and how to implement it through the control variables? Is the internal energy shown as EGB in each step in the output file?
I am using Amber14 and have checked the directory amber14/test/gbsa_xfin. But I am not sure if this is the input file that I should be applying to my system.
I already apologize if this question has been addressed before.
Thanks in advance
Ramin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 03 2017 - 18:30:02 PDT
