From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Tue Aug 23 2011 - 19:47:25 CDT
pretty sure this isn't a bug in namd...
On Tue, Aug 23, 2011 at 6:28 PM, <wenhao_at_uchicago.edu> wrote:
> I've set up a system of 2 sodium ions in Vacuum which are fixed in 8 angstrom for a check. I do the minimization and FEP to calculate the electrostatic energy. I've set alchVdwLambdaEnd and alchElecLambdaStart all 0(or all 0.5 but the result are the same) so as to consider the electrostatic energy only which should be equal to Columb energy(41.5kcal/mol). But the result is just about 20 kcal/mol the cutoff, switchdist, pairlistdist are 15, 14 and 16. And when I set the cutoff, switchdist, pairlistdist larger, namd will give a lager value.
> Whetehr in PME or noPME, the value are all much smaller than 40. And to be easy, just see the elec energy value in Minimization log, we can also see that it is much smaller than the Columb energy. NAMD can not calculate the Columb erergy between 2 ions, is this a bug in namd?
> Thanks a lot.
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