From: yjcoshc (yjcoshc_at_gmail.com)
Date: Sun Jul 26 2020 - 12:58:50 CDT
Hi Qasim,
The namd2_ti.pl is outdated. I have some C++ code for parsing it. You
may have a look at https://github.com/HanatoK/TI , and just compile it
with "g++ TI.cpp -std=c++17 -o ti" and then run "./ti
<your_ti_output_file>" for analysing the TI output.
Anyway, I seldom use the TI estimator for alchemical transformations
since TI requires lots of small windows, and it lacks the benefits from
BAR or MBAR estimator.
Best regards,
Haochuan Chen
在 2020/7/25 下午11:42, Qasim Pars 写道:
> Dear users,
>
> I calculated the hydration free energy of a molecule using NAMD-2.13
> with the thermodynamic integration method. My ti.out file looks like this:
>
> #TITITLE: TS BOND1 AVGBOND1 ELECT1 AVGELECT1
> VDW1 AVGVDW1 BOND2 AVGBOND2
> ELECT2 AVGELECT2 VDW2 AVGVDW2
> #NEW TI WINDOW: LAMBDA 0
> #PARTITION 1 SCALING: BOND 1 VDW 0 ELEC 0
> #PARTITION 2 SCALING: BOND 1 VDW 1 ELEC 1
> #CONSTANT TEMPERATURE: 298.15 K
> TI: 0 0.0000 0.0000 -6.1675
> -6.1675 -5.5010 -5.5010 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000
> TI: 100 0.0000 0.0000 -5.7933
> -5.7970 -5.5389 -5.5385 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000
> TI: 200 0.0000 0.0000 -3.9530
> -4.8796 -5.0426 -5.2918 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000
> TI: 300 0.0000 0.0000 1.7023
> -2.6929 -4.6941 -5.0932 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000
> ...
>
> When I run namd2_ti.pl <http://namd2_ti.pl> script, I get the below
> error. Does anyone know how to fix this error? Or does anyone have
> another script to calculate the free energy from the ti.out file of NAMD?
> Here is the error after running ./namd2_ti.pl <http://namd2_ti.pl>
> ti.out :
> Found 1 output files
> Reading files: .Output file ti.out not recognised as a NAMD TI output file
> No usable TI output files found - check presence of files in current
> directory make sure the correct extension is specified (--extension)
>
> Thanks in advance,
>
> --
> Qasim Pars
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