Gerrit Groenhof wrote:
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Is there an implementation in gromacs for using a uniform neutralizing
plasma with PME, to avoid use of counterions?
Thank you
-Himanshu
Neutralization is done implicitly, by omitting out the zeroth plane
wavevector (m=0, see sec. 4.6 of the gmx manual). However, it is
advisable to use explicit ions always, as the neutralizing background
charge leads to artefacts.
However, if you do, you should probably add ions to match the ionic
strength in your solution. See e.g.
"Incorporating the effect of ionic strength in free energy calculations
using explicit ions"
Author(s): Donnini S, Mark AE, Juffer AH, Villa A
Source: JOURNAL OF COMPUTATIONAL CHEMISTRY Volume: 26 Issue: 2
Pages: 115-122 Published: JAN 30 2005
BEst,
Gerrit
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