From: Qasim Pars (qasimpars_at_gmail.com)
Date: Tue Jul 28 2020 - 15:01:12 CDT
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 The namd2_ti.pl is outdated.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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