AMBER Archive (2004)

Subject: Re: AMBER: Regarding Dielectric Constant in AMBER8

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Nov 26 2004 - 10:55:48 CST


pande.vineet_at_fc.up.pt wrote:

>
>The calculation runs beyond perfection, structure is quite reasonable :)... This
>means that with eedmeth=5 in the ewald part and dielc = 4, in the upper section
>we are actually implementing a distance-dependent dielctric 4r(i,j), right? One
>
>
yes, this is a distance dependent dielectric. sander should
tell you this, please read the output files carefully.

>another question.. In this non-periodic case of ewald sums, how shall i decide
>for example on other PME flags like USE_PME (which I usually put 0 for PBCs to
>
>
use_pme won't matter, your sander output should already say that pme isn't
used since it isn't periodic.

>save time..), and VDWMETH..? Shall they remain defaults, like I used in this
>test?
>
>
you say that you usually set use_pme to 0 to "save time", but you
should also consider the quality of the calculation, not just the speed.
many studies have shown that long-range interactions can be important.
carlos

>Thanks again,
>Kind Regards
>Vineet
>
>
>
>omo_at_scripps.edu
>
>
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