Dear Amber mailing list,
As a novice to the AMBER software I ran into a problem regarding the
manual parameterization of the TIP4P/2005 water model by Abascal and Vega.
I was searching through the mailing list and found a thread from 2013
addressing this problem.
http://archive.ambermd.org/201310/0410.html
Now I do have some follow-up questions regarding the manipulation of the
files:
Basicially I would only need to modify/copy the frcmod.tip4pew (for
instance to frcmod.tip4p2005) and the tip4pewbox.off (e.g.
tip4p2005box.off) in the respective dat/leap/parm and dat/leap/lib
folders, is that correct?
The original publication of Abascal and Vega reports that four
parameters have been readjusted and changed from TIP4P/Ew to TIP4P/2005,
which both share the same geometry and functionality: The strength ε and
size σ of the LJ center, the hydrogen site charge (or the charge of the
M site, qh=-qm/2) and the distance dOM between the oxygen and the M site.
The dOM distance is apparently set through the BOND OW-EP value in the
third column (from 0.1250 to 0.1546) in the frcmod.tip4pew file.
The hydrogen site charge can be changed in the tip4pewbox.off file - all
the values of "H1" and "H2" adjusted from 0.524220 to 0.556400 and the
values of EPW from -1.048440 to -1.112800.
But where can I incorporate the changes of the LJ interaction parameters
ε (set from 81.9 to 93.2) and σ (set from 3.16435 to 3.1589), which are
stated in the publication in TABLE I? I have not been successful in
finding the numerical values in either one of the files?
Sorry for this naive question and thank you in advance for your help.
Hannes
--
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HK
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Received on Thu Jul 27 2017 - 07:30:03 PDT
