Egb in the output file is just the solvation free energy.
On Apr 4, 2017 10:50 AM, "Ramin Salimi" <ramin.salimi01.utrgv.edu> wrote:
Hi Dr. Case
I appreciate your reply
But I am a bit confused. When we calculate the total free energy of our
system, we write it as Gtot = Eintra + Gsolv - TSintra , and we want to
calculate the internal energy, we cannot unambiguously separate out the two
contributions
Eintra + Gsolv . Am I right? If so, can we say that the EGB shown in the
output file of the GB/SA method is the sum of these two terms? or it is
just Gsolv? If it just the Gsolv, how can we find the contributions solely
from internal energy?
Kind Regards
Ramin
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, April 4, 2017 7:17:39 AM
To: AMBER Mailing List
Subject: Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal
energy
On Tue, Apr 04, 2017, Ramin Salimi wrote:
>
> 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
The best thing to read is Chapter 4 of the 2016 Reference Manual (and you
should go ahead and download/install AmberTools16.) We recommend using
igb=8
for both proteins and nucleic acids.
>
> 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?
EGB is the estimated solvation free energy, which is added to all the other
terms to get the total potential energy.
> 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.
That is a good example input, but see the comments above about igb.
Tutorial
B3 also walks you through running a GBSA simulation.
...hope this helps...dac
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Received on Tue Apr 04 2017 - 14:30:03 PDT
