Re: Output of thermodynamic integration

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Jan 28 2012 - 04:25:19 CST

Dear Kei-ichi,

If you are decoupling the solute from the solvent, it probably has -1
flags in the alchFile. In this case, the lambdas for the solute are
reversed with respect to the "global" lambda, and the first thing that
happens is that electrostatics gets decoupled (which is the right
thing to do).

Best,
Jerome

On 28 January 2012 01:16, Kei-ichi Okazaki <keiichi.okazaki_at_nih.gov> wrote:
> Dear NAMD users,
>
> I am trying to calculate solvation free energy of a small molecule by
> thermodynamic integration (TI).
> And I have a question about output file of TI.
> I set up configuration file for TI with soft-core potential as below.
> I set "alchElecLambdaStart 0.5" and "alchVdwLambdaEnd 0.5" to separate the
> scaling of vdW and electrostatics, that is, vdW is turned on first for
> 0<=lambda<=0.5 and then, ele is turned on for 0.5<=lambda<=1.0.
> And in the output, Elec_dU/dl and vdW_dU/dl are reported as below.
> When I saw the output of lambda=0.1, for example, I was confused because
> Elec_dU/dl takes some values even though ele is not turned on yet.
> I suspect that it just reports Elec_dU/dl for lambda=0.0, but it cannot be
> used for TI calculation because there should not be any contribution from
> ele for lambda<0.5.
> Is my guess right? I appreciate any suggestions.
>
> Thanks in advance.
> Kei-ichi Okazaki, PhD
>
> ## configuration file #########################################
> # Free energy perturbation
> alch           On             # Enable alchemical simulation module
> alchType       ti             # Set method to thermodynamic integration
> alchFile       ../../Common/h2p.box20.alchem.pdb   # PDB file with
> perturbation flags
> alchCol        B              # Perturbation flags in Beta column
> alchOutfile    $outputname.out
> alchOutFreq    1000
> alchEquilSteps 500000
>
> alchVdWShiftCoeff    6.0       # Enable soft-core vdW potential
> alchElecLambdaStart  0.5       # Introduce electrostatics for lambda > 0.0
> alchVdwLambdaEnd     0.5
> alchLambda 0.1
> alchLambda2 0.1
>
> ## output file #################################################
> #       STEP      Elec_dU/dl      Elec_avg        vdW_dU/dl      vdw_avg
>   Elec_dU/dl      Elec_avg      vdW_dU/dl       vdw_avg       PME_dU/dl
>  PME_avg
> # <---------------------PARTITION 1------------------------>
> <---------------------PARTITION 2--------------------->
> #NEW TI WINDOW: LAMBDA 0.1
> #PARTITION 1 VDW LAMBDA 0.2
> #PARTITION 1 ELEC LAMBDA 0
> #PARTITION 2 VDW LAMBDA 1
> #PARTITION 2 ELEC LAMBDA 0.8
>
> TI        0       -452.9840      -452.9840        -9.6522        -9.6522
>     0.0000         0.0000         0.0000         0.0000
> TI     1000       -228.3854      -228.6098         1.7409         1.7296
>     0.0000         0.0000         0.0000         0.0000
>

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