The softcore scheme in AMBER does not include electrostatic and non-bonded contributions between softcore atoms but computes those only with the environment. So, the vaccum calculation will always be zero in case the whole morph pair is in the TI region. Just try it out!
I am not aware that these contributions could be switched on as in other codes.
I think the correction term for 2. is in relation to a 2-step absolute solvation scheme where the whole molecule is discharged before a vdW-only transformation, right?
Cheers,
Hannes.
________________________________________
From: Teerapong Pirojsirikul [tpirojsi.ucsd.edu]
Sent: 01 January 2015 01:08
To: AMBER Mailing List
Subject: [AMBER] Solvation free energy using soft core potential
Hi AMBER users,
I am currently working on solvation free energy using the soft core
potential and trying to reproduce some results from a paper. I have a few
questions as follows.
1. According to the following thread,
http://structbio.vanderbilt.edu/archives/amber-archive/2008/2574.php, and
as explained by Dr. Steinbrecher, it seems to me that we don't need to
perform the calculation for dG1 (in the scheme drawn by yongleli), and it
accounts for zero. In this case, is the dG(solv) = dG3(molecule in gas to
molecule in water) = -dG2(molecule in water to nothing in water) then
(because dG1(molecule in gas to nothing in gas) = dG4(nothing in gas to
nothing in water) = 0)? If this is the case, does this also mean we don't
need to perform vdw interaction removal of the molecule in vacuum at all
when employing the soft core potential? Please correct me if I am wrong.
2. In contrast to the first question, in the paper "Nonlinear scaling
schemes for Lennard-Jones interactions in free energy calculations" by Dr.
Steinbrecher et al., there suggests that the correction of molecule
dissapearing in vacuum would be evaluated and substracted from the free
energy of molecule dissapering in water. The setup for the latter part is
straightforward, which is creating a moleculate in the water box and pure
water box as end states (as also done by yongleli in the thread above).
However, in vacuum, how would we setup the system to get the correction
free energy unless we create a dummy atom as an end state?
Best,
Tee
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Received on Thu Jan 01 2015 - 07:30:02 PST
