Re: regarding ion concentration in implicit solvent

From: Prathit Chatterjee (
Date: Wed Feb 29 2012 - 08:04:08 CST

Dear NAMD Experts, Few days ago I had asked a question regarding ion-concentration and its implications of making a system neutral in implicit solevnt if possible and/or required. My mail is stated below.  I would highly appreciate the endeavor if someone enlightens me of this. Thanking You Prathit ________________________________ From: Prathit Chatterjee <> To: NAMD Mailing list <> Sent: Friday, 24 February 2012 4:49 PM Subject: namd-l: regarding ion concentration in implicit solvent 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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:42 CST