Re: [AMBER] Calculation of Urea_Urea Interaction energy

Date: Fri, 5 Sep 2014 23:36:27 +0530

Dear Jason

Thank you for help

> Dear Amber Users
> I want to calculate interaction energy between two urea molecules in
> homogeneous urea solution (only urea molecules are there). For that I used
> antechamber modules to generate urea "prep" and "frc" file. The generated
> file contain GAFF force field parameter. After production MD run, I
> the trajectory to calculate pairwise interaction energy. I used the
> pairwise command but I am getting + 36.34 kcal/mol while the reported
> theoretical value for dimer is -10.33 kcal/mol (MP2/aug-cc-pVDZ).
> I am using "CPPTRAJ: Trajectory Analysis. V13.0".

What's the actual command you're using? (Not just the command name, the
_full_ command).

I am using the following command

cpptraj -p -i


trajin ../md_file/

reference ../md_file/urea

pairwise U_U :URA out pairwise_
.txt cuteelec 12.0 cutevdw 12.0

Is there are bugs in this command??

cpptraj is part of Amber. Amber has no bugs. So cpptraj has no bugs.

Kidding, of course, but in cases like this I've found that it's best to
assume I don't fully understand what I'm computing or exactly what I asked
the program to compute. This is why knowing the exact command is important.

Also, there's no reason to expect that two urea molecules in bulk urea have
the same interaction as the urea dimer... You're also comparing a minimum
energy structure (MP2/aug-cc-pVDZ) with what is likely an ensemble property
if you're computing this value over a trajectory. When doing comparisons
like this, it's very important that you make every effort to make sure you
are making a fair comparison.

​The main point is that, How urea interaction energy showing positive value
It means that the system is thermodynamically very unstable due to positive
interaction energy (unfavorable interaction). The value should be equal to
or below zero in any range (never exactly match with quantum calculation)
because we are calculating over trajectory.

Or may be the high positive Interaction value arise due to wrong non-bonded
parameter. ​

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Received on Fri Sep 05 2014 - 11:30:02 PDT
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