From: Mateusz Bieniek (bieniekmat_at_gmail.com)
Date: Wed Jul 29 2020 - 09:14:53 CDT
I am afraid I am not using this script in general. So it would only be a
starting point. Using Haochuan code might work better.
I tweaked it before to check the tools I was developing. I can't promise
much, but if you share some example input files and the command that you
use, I can try to have a quick look.
Best, Mat
On Tue, 28 Jul 2020 at 21:01, Qasim Pars <qasimpars_at_gmail.com> wrote:
> Hi,
>
> Thanks Haochuan and Mateusz.
>
> Mateusz: Checked your script. It works properly. You said "It currently
> ignores bonds..." but unfortunately I don't know how to fix your script to
> take into account bonds as well as VDW and ELE. Do you have the fixed
> script?
> Apart from that, for 0->1 state I got a value of -2.0 kcal/mol and as for
> 1->0 state I got a value of -4.0 kcal/mol with your script. Should I take
> the average of -2.0 and -4.0 kcal/mol to calculate the hydration free
> energy from the forward and backward state?
>
> Best,
>
> On Sun, 26 Jul 2020 at 21:38, Mateusz Bieniek <bieniekmat_at_gmail.com>
> wrote:
>
>> Hi Qasim,
>>
>> Here is a partly updated script which can be a good starting point to
>> change the namd2_ti.ph script. It currently ignores bonds, and only
>> takes into account the VDW and ELE to calculate the dG.
>>
>> See comments in the code for more.
>>
>>
>> Best,
>> Mateusz Bieniek
>>
>> On Sun, 26 Jul 2020 at 19:00, yjcoshc <yjcoshc_at_gmail.com> wrote:
>>
>>> 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 The namd2_ti.pl is outdated.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 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 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
>>>
>>>
>
> --
> Qasim Pars
>
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