[gmx-users] Re: Drug-Enzyme tutorial- LIE energies in gromacs
n.gandhiau at gmail.com
Wed Mar 25 06:24:23 CET 2009
In the same tutorial I find the comment (caution) about use of PME with full
periodic boundary conditions (PBC) with LIE method.
I have seen the recent papers by Johan Aqvist and they use reaction field
approximation for long range electrostatics without PBC and using NPT
I was wondering if there are reports where LIE has been parameterise using
PME and PBC.
Thanks and Regards,
2009/3/24 Neha Gandhi <n.gandhiau at gmail.com>
> Dear GMX-users,
> In the Gromacs Drug/Enzyme complex solvation tutorial by John E. Kerrigan ,
> in the end they mention about the LIE calculation. The g_lie program uses
> LIE equation with default scaling factors a=0.18 and b=0.50 . In the
> tutorial it is mentioned that For example, b = 0.33 is preferred for polar
> solutes (drugs) like sugars. What is the reference for these values for
> polar solutes i.e. sugars.? I would appreciate if there is any example of
> such calculation done in gromacs.
> Many thanks,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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