[AMBER] gas phase TI

From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
Date: Tue, 19 Feb 2019 16:42:00 +0100

I wanted to calculate the difference in the hydration free energy of ethane
and ethanol, so I did one-step mutation TI for the solvated ethane and
ethanol, and in the gas phase using the whole molecules as TI region and
soft-core region, but in the gas phase there is no DV/DL reported in the
output, and MBAR energy is zero. When I use just the hydrogen of ethane and
O,H of ethanol as TI region and soft-core region then it works. I thought
it might be because I am transforming from ethane which all of its bonded
interactions are excluded, is that the reason?? Because the final result is
not correct, but I cannot figure it out what is the reason. What are the
things to consider while doing the gas phase with TI???

Another question is, how can I use MBAR energy produced by TI calculation
in my output to get the entropy and other values from the BAR method?? Is
there any script for that??

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Received on Tue Feb 19 2019 - 08:00:04 PST
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