From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Fri Feb 24 2012 - 05:19:51 CST
Dear NAMD Experts,
I want to simulate a peptide in implicit solvent using NAMD_2.8. I needed 8 Na+ ( ~0.04 M of Na+) ions to neutralize the overall system while using explicit solvent.
But, in implicit solvent, specifying ion-concentration means adding that much of a monovalent salt in the implicit solvated system (as specified in the NAMD manual).
So, is it necessary to neutralize the system even in implicit solvent and if so how? Also I need to know the implication of ion-concentration in an implicitly solvated system.
Any kind of advice/ suggestions will be deeply appreciated.
Thanks in Advance
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