[AMBER] Gas phase simulation for heat of vaporization calculation

From: <wijaya.t.aa.m.titech.ac.jp>
Date: Wed, 5 Feb 2020 17:18:20 +0900

Dear all,


I want to calculate heat of vaporization of tricaprylin. I am following the
steps in lipid14 paper. Heat of vaporization can be calculated by this


deltaHvap = Epot(g) - Epot(l) + RT


According to the paper, "A gas phase simulation consisting of a single
alkane molecule was run for 10 ns equilibration and 50 ns production under
the NPT ensemble, at a temperature of 298.15 K to obtain Epot(g)". However,
to run NPT di amber18, I need to set ntb=2 and provide periodic box in the
coordinates file. However, as long as I understand, since the equation
assumes V(g) >> V(l), how big the box should be? If I use standard protocol,
which is to set box dimensions in the distance of more than cut-off, is it
not big enough to satisfy the assumption?


Or is it okay if I just run a no-pbc, NVT, single molecule simulation with
infinite cutoff to get Epot(g)?


Thank you



Tegar N W

AMBER mailing list
Received on Wed Feb 05 2020 - 00:30:02 PST
Custom Search