From: Brian Radak (bradak_at_anl.gov)
Date: Thu Aug 03 2017 - 08:20:36 CDT
It is perfectly possible to overlap the regions or have them be
completely concurrent. For example, the following will give you
concurrent /linear/ coupling:
I prefer to think of the coupling coefficients as functions dependent on
vdw_couple = min[1, alchLambda / alchVdwLambdaEnd]
elec_couple = max[0, (alchLambda - alchElecLambdaStart) / (1 -
The group 1 interactions are scaled by xxx_couple(alchLambda) and the
group -1 interactions are scaled by xxx_couple(1 - alchLambda).
New in NAMD2.12 (or maybe it was 2.11) there is now a coupling for
bonded terms that is completely analogous to vdW coupling. This is off
by default because alchBondLambdaEnd is set to 0.0. You can also turn
off vdW scaling with the same trick or turn off elec scaling by setting
On 08/02/2017 04:18 PM, John Green wrote:
> I am trying to set up soft-core parameters for an FEP simulation. This
> is how this part of input file looks like:
> alchElecLambdaStart 0.5
> Based on tutorial, my understanding is that coupling and decoupling of
> electrostatic interaction for disappearing and appearing particles
> _always_ occur in two separate periods.
> [ 0 (1-alchElecLambdaStart) ] & [ (1-alchElecLambdaStart) 1 ]
> While for VDW you can have coupling and decoupling at the same time.
> [ (1-alchVdwLambdaEnd) 1 ] & [0 (1-alchVdwLambdaEnd) ]
> Is there any option to do that for electrostatic interactions as well?
> The manual says the default for alchElecLambdaStart is 0.5, so even if
> I don't use it in my script it wouldn't be helpful.
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
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