you always need to consider uncertainty when comparing 2 methods.
the question here is really: is the variation between CG and TNCG results
*larger* than the variation between multiple runs using a single method?
the difference you see could very well just be run to run variation
(precision) and not at all an indicator of differences caused by the method.
On Sat, Nov 12, 2011 at 10:20 AM, Anglea A. <a.anglea90.yahoo.com> wrote:
> Hi All
> I run MD simulation of protein-ligand complex for 1ns. The system was
> initially equilibrated and minimized using CG and SD method.
> The calculation was re-done using the same conditions, except the system
> was minimized this time using TNCG method.
> The difference between the calculated GBSA energies for the two
> calculations was around 0.8 kcal/mol.
> Is that normal? and what the scientific reason behind it?
> Cheers
>
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Received on Sat Nov 12 2011 - 07:30:04 PST
