Re: error with namd2_ti.pl script

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The namd2_ti.pl is outdated.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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