From: John Green (john.green.jr1982_at_gmail.com)
Date: Thu Aug 03 2017 - 12:49:20 CDT
Thank you very much again. Still I think the example in user guide doesn't
follow the above calculation since the calculation says decoupling is
happening from 0.5 to 1 but in the picture (even considering we just have
decoupling) decoupling happens at the first half.
My question is regarding the overlap in electrostatic coupling and
decoupling itself. Could we overlap or separate them (regardless of the
LJ)? or we always have them at the same time?
On Thu, Aug 3, 2017 at 12:02 PM, Brian Radak <bradak_at_anl.gov> wrote:
> The conversions you show are correct - I'm not exactly sure what is
> confusing here (although the whole thing can be a bit confusing). I think
> the trouble is that the left hand plot in the user guide assumes that you
> only have one alchemical group (group -1 in that case) so that only
> "decoupling" is occurring.
>
> The real question is how much do you want electrostatic and van der Waal
> decoupling to overlap? Turning off the electrostatics completely before
> modifying vdW can be excessive and result in an inordinate number of
> alchLambda values. If you want to go that route, I'm not sure that you can
> run a single set of simulations since you would have to use
> "alchVdwLambdaEnd 0.0" for the first part and then change the value to 1.0
> later.
>
> There has been some talk of updating some of these scheduling options,
> including adding decomposition of the vdW terms into attractive and
> repulsive components.
>
> Does that help?
>
> Brian
>
> On 08/03/2017 11:38 AM, John Green wrote:
>
> 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
>>
>
>
> --
> 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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