Re: Setting up softcore parameters for FEP

From: Brian Radak (bradak_at_anl.gov)
Date: Thu Aug 03 2017 - 12:02:47 CDT

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
> <mailto: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:
>>
>> alchVdwLambdaEnd1.0
>>
>> alchElecLambdaStart 0.5
>>
>> alchVdWShiftCoeff5.0
>>
>> alchDecoupleno
>>
>>
>> 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 <tel:%28630%29%20252-8643>
> brian.radak_at_anl.gov <mailto: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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