AMBER Archive (2009)

Subject: Re: [AMBER] Regarding united atom force field

From: FyD (
Date: Tue Sep 22 2009 - 01:13:03 CDT

Dear Aeesh,

> I would like to use united atom model for simulation of
> n-alkanes. Which force filed will be the better one?. can anyone suggest
> some reference for the same.

- I suggest you to read:
Failure of net atomic charge models to represent the van der Waals
envelope electric potential of n-alkanes
Donald E. Williams Volume 15 Issue 7, Pages 719 - 732

- Then, you could use R.E.D.-III.x to generate RESP charges within
force field libraries. A way would be to use intra-molecular charge
constraint(s) set to zero for each hydrogen + with the R (Remove) flag.
Two other approaches for generating united-atom force field libraries
will be available soon in R.E.D. IV/R.E.D. Server (two last approaches
are in development).

regards, Francois

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