From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
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 <pc20apr_at_yahoo.co.in>
To: NAMD Mailing list <namd-l_at_ks.uiuc.edu>
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
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