On Sun, Feb 05, 2017, Liyang Zhu wrote:
> Typically the VDW parameters in Amber is as follows:
>
> * angstrom kcal/mol *
> c1 1.9525 0.1596
> *o 1.7101 0.1463*
>
> And get to know that there is a EPM2 model for CO2 used in many papers,
> which is high accurate for density properties. However, the parameters can
> not be used in amber correctly, because there is always a error of sander
> bomb during NTP equilibrium. The parameter of EPM2 is as follows:
>
> * angstrom kcal/mol *
> c1 2.757 0.0558
> *o 3.033 0.1600*
The Amber Rmin parameters in force field files are actually Rmin/2: that is,
they are atomic radii, not diameters. You don't say what you actually did,
but that might be a part of the problem. If the EPM2 number above is
a sigma value(?), then the Rmin value Amber needs is 3.033*(2**1/6)/2
= 1.702, which is close to the GAFF value you cite above.
If this is not the problem, then you would need to give more information: just
saying "sander bomb" doesn't allow those on the list to offer much real help.
....dac
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Received on Mon Feb 06 2017 - 08:30:02 PST
