From: John Green (john.green.jr1982_at_gmail.com)
Date: Thu Aug 03 2017 - 11:38:37 CDT
Thank you very much. Let's focus on electrostatic coupling for a moment.
Let's say:
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
So according to the formula you mentioned we have :
elec_couple=max(0,2*lambda-1)
lambda=0 --> elec_couple=0 , elec_decouple=1
lambda=0.5 --> elec_couple=0 , elec_decouple=1
ambda=1 --> elec_couple=1 , elec_decouple=0
So both decoupling and coupling happen between lambda (0.5 to 1). But the
left figure in this page shows that decoupling happens at the first half (0
to 0.5)
http://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node61.html
Did I miss something here?
Best,
JJ
On Thu, Aug 3, 2017 at 8:20 AM, Brian Radak <bradak_at_anl.gov> wrote:
> Hi John,
>
> It is perfectly possible to overlap the regions or have them be completely
> concurrent. For example, the following will give you concurrent *linear*
> coupling:
> alchVdwLambdaEnd 1.0
> alchVdwShiftCoeff 0.0
> alchElecLambdaStart 0.0
>
> I prefer to think of the coupling coefficients as functions dependent on
> alchLambda:
>
> vdw_couple = min[1, alchLambda / alchVdwLambdaEnd]
> elec_couple = max[0, (alchLambda - alchElecLambdaStart) / (1 -
> alchElecLambdaStart)]
>
> 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 alchElecLambdaStart
> 1.0.
>
> HTH,
> Brian
>
>
> On 08/02/2017 04:18 PM, John Green wrote:
>
> Hi,
>
> I am trying to set up soft-core parameters for an FEP simulation. This is
> how this part of input file looks like:
>
> alchVdwLambdaEnd 1.0
>
> alchElecLambdaStart 0.5
>
> alchVdWShiftCoeff 5.0
>
> alchDecouple no
>
>
> 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.
>
>
> Best,
>
> John
>
>
>
> --
> 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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