Thank you for your response, I think I could manage to determine the
correct parameters now.
> The LJ parameters for the oxygen atom (type OW) are in the frcmod.tip4pew
> file, in the "NONBON" section. Details on the representation of LJ
> parameters
> are given here:
>
> ambermd.org/Questions/vdwequation.pdf
>
> ...good luck...dac
Nevertheless, I want to share some additional information, which might
be interesting for other AMBER users with a similar problem:
The conversion from σ[Å] to r0 [Å] worked as described in the provided
link, but note that only the halved value gets specified in the frcmod
file in the OW atom type line in the OW section. Hence for the
TIP4P/2005 water model I could finally set the numeric value of the OW
atom type to 1.772873 Å.
In the previously mentioned publication, the depth of the well was given
in ε/k [K]. This reduced quantity can be converted to the ε used by
AMBER via the Boltzmann constant k [kcal/(mol*K)]. For TIP4P/2005 I came
up with a ε = 0.185207.
Yesterday I got to know, that ready to use parameter files for the
TIP4P/2005 water model have been uploaded to the GitHub repository of
Robert Best with more or less the same values that I got. Best uses
TIP4P/2005 along with his modified force field ff03ws for the simulation
of IDPs and protein unfolding.
https://github.com/bestlab/force_fields/tree/master/amber_format
Best regards,
Hannes
--
========================================================================
HK
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Received on Wed Aug 02 2017 - 01:30:02 PDT
