regarding ion concentration in implicit solvent

From: Prathit Chatterjee (
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 Prathit

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