Re: How to interpret Thermodynamic Integration output

From: Brian Radak (brian.radak_at_gmail.com)
Date: Sun Feb 25 2018 - 12:45:10 CST

Hi Sadegh,

Yes, this is indeed a slightly undocumented update in the latest version
(though not much less documented than the old version).

The derivatives are separated by alchemical groups (group 1 is scaled with
lambda and group 2 is scaled with 1 - lambda, these are specified in the
input PDB with 1 and -1).

Note also that *everything in the alchOutFile is an average*. The normal
output is a local/block average over the last alchOutFreq steps and the AVG
columns are cumulative averages. There's really no good reason to have
alchOutFreq as small as you have it - it just hurts performance due to
frequent I/O.

It is up to the user to decide what they want to do with the output. If you
are using simple trapezoidal integration, you would have to scale each
column according to the appropriate deltaLambda increment (which you have
to compute yourself).

HTH,
BKR

P.S. Note also that the instantaneous TI derivatives are now also sent to
stdout according to outputEnergies. You can safely suppress all output to
alchOutFile by setting alchOutFreq 0 and just use the stdout if you prefer
- I sincerely doubt you would be able to detect a difference in the
analysis of any reasonable calculation.

On Fri, Feb 23, 2018 at 7:09 PM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad_at_mix.wvu.edu> wrote:

> Hello all,
>
> I have done a TI calculation, but can't find any tutorial or document
> about how to interpret the output. Here is how my output file starts
>
> #TITITLE: TS BOND1 AVGBOND1 ELECT1
> AVGELECT1 VDW1 AVGVDW1 BOND2 AVGBOND2
> ELECT2 AVGELECT2 VDW2 AVGVDW2
> #NEW TI WINDOW: LAMBDA 0
> #PARTITION 1 SCALING: BOND 0 VDW 0 ELEC 0
> #PARTITION 2 SCALING: BOND 1 VDW 1 ELEC 1
> #CONSTANT TEMPERATURE: 310 K
> TI: 0 19.7158 19.7158 -31.3316
> -31.3316 -6.5855 -6.5855 12.4099 12.4099
> -40.2905 -40.2905 21.8477 21.8477
> TI: 10 19.4744 19.4964 -31.2402
> -31.2486 -6.5801 -6.5806 10.7752 10.9238
> -40.0014 -40.0277 18.3626 18.6795
> TI: 20 24.9347 22.0861 -29.0597
> -30.2062 -6.5748 -6.5778 10.0471 10.5063
> -38.9418 -39.5106 12.0912 15.5422
> TI: 30 32.2653 25.3697 -25.5063
> -28.6901 -6.5840 -6.5798 9.2265 10.0935
> -38.3273 -39.1289 10.4395 13.8962
> TI: 40 42.3413 29.5091 -20.9719
> -26.8077 -6.6005 -6.5848 9.9239 10.0521
> -38.7601 -39.0389 13.5623 13.8147
> TI: 50 58.5311 35.1997 -15.9560
> -24.6799 -6.6079 -6.5894 11.9345 10.4212
> -39.2660 -39.0835 12.5075 13.5584
> TI: 60 80.3605 42.6031 -12.8759
> -22.7448 -6.6090 -6.5926 10.8168 10.4861
> -39.5107 -39.1535 6.7353 12.4399
> TI: 70 102.0040 50.9694 -14.6704
> -21.6076 -6.6234 -6.5969 10.6856 10.5142
> -39.9275 -39.2625 5.4385 11.4538
> TI: 80 119.1639 59.3885 -20.0657
> -21.4172 -6.6514 -6.6037 12.3398 10.7396
> -39.4442 -39.2849 8.3762 11.0738
> TI: 90 130.3328 67.1846 -23.9356
> -21.6940 -6.6710 -6.6111 9.7465 10.6304
> -37.6627 -39.1067 11.6755 11.1399
> #100 STEPS OF EQUILIBRATION AT LAMBDA 0 COMPLETED
> #STARTING COLLECTION OF ENSEMBLE AVERAGE
> TI: 100 127.3925 127.3925 -23.4962
> -23.4962 -6.6485 -6.6485 9.9449 9.9449
> -37.7934 -37.7934 9.3023 9.3023
> TI: 110 123.5767 123.9236 -23.1205
> -23.1546 -6.6329 -6.6343 10.3050 10.2723
> -39.3857 -39.2410 6.6564 6.8969
>
> It seems like BOND1 and BOND2 etc. are for the initial and final values of
> lambda, respectively. If so, is AVGBOND1+AVGELECT1+AVGVDW1 the total TI
> energy for each timestep? then if I sum the total energies of all timesteps
> I will get the total TI for the total transition from lambda=0 to lambda=1?
>
> Thanks in advance,
> Sadegh
>
>

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