Re: Output of thermodynamic integration

From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Jan 29 2012 - 16:08:41 CST

Kei-ichi,

I think it's a bug and have opened it as a bug-issue. Can you please send
me as a tar.gz the files needed to replicate exactly *your* result.

Best,
Chris

On Sun, Jan 29, 2012 at 2:22 PM, Okazaki, Keiichi (NIH/NIDDK) [F] <
keiichi.okazaki_at_nih.gov> wrote:

> Dear Jerome and developers,
>
> Thank you for your help!
> I think there is a similar problem also for vdW_dU/dl.
> Since vdW is turned on first for 0<=lambda<=0.5 in my case, I expect that
> vdW doesn't contribute for lambda>0.5, where LJ potential is independent on
> lambda.
> But it's not in output file, for example, lambda=0.9 shown below.
> If my guess is right, I think it is not a serious bug, but confusing.
> Can I just ignore Elec_dU/dl for lambda<0.5 and vdW_dU/dl for lambda>0.5??
>
> Regards,
> Kei-ichi
>
> ## 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 0.9
> #PARTITION 1 VDW LAMBDA 1
> #PARTITION 1 ELEC LAMBDA 0.8
> #PARTITION 2 VDW LAMBDA 0.2
> #PARTITION 2 ELEC LAMBDA 0
>
> TI 0 -452.9840 -452.9840 97.2694 97.2694
> 0.0000 0.0000 0.0000 0.0000
> TI 1000 -390.6807 -390.7429 66.7038 66.7344
> 0.0000 0.0000 0.0000 0.0000
>
> ________________________________________
> From: heninj_at_gmail.com [heninj_at_gmail.com] On Behalf Of Jérôme Hénin [
> jhenin_at_ifr88.cnrs-mrs.fr]
> Sent: Saturday, January 28, 2012 1:52 PM
> To: Okazaki, Keiichi (NIH/NIDDK) [F]
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Output of thermodynamic integration
>
> You are right, I should have seen it in the output you attached. This
> is beginning to look like a bug. I don't know the TI code well, and I
> don't have the time to go into the details right now. I hope that
> another developer can chime in...
>
> Best,
> Jerome
>
>
> On 28 January 2012 17:31, Okazaki, Keiichi (NIH/NIDDK) [F]
> <keiichi.okazaki_at_nih.gov> wrote:
> > Dear Jerome,
> >
> > Thank you for your suggestion.
> > However, 1 is set in my alchFile for the flag, that is, it goes in the
> same direction with the global lambda.
> > So, I am still not sure why Elec_dU/dl takes some values even though ele
> is not turned on yet.
> >
> > Regards,
> > Kei-ichi
> > ________________________________________
> > From: heninj_at_gmail.com [heninj_at_gmail.com] On Behalf Of Jérôme Hénin [
> jhenin_at_ifr88.cnrs-mrs.fr]
> > Sent: Saturday, January 28, 2012 5:25 AM
> > To: Okazaki, Keiichi (NIH/NIDDK) [F]
> > Cc: namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: Output of thermodynamic integration
> >
> > 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--e89a8f3bac3d03090a04b7b1f948--

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