CCL: MD simulation of charged systems

["Venable, Richard (NIH/NHLBI) [E]" <venabler(-)nhlbi.nih.gov>]

 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]"
 [venabler::nhlbi.nih.gov]
 Yes, there may be objections.
 In general, P-M Ewald should be used with net neutral systems, usually achieved
 by adding some number of aqueous ions; depending on the system context and its
 geometry, 100-200 mM of added salt is often a good idea as well.
 There are provisions in some MD programs for dealing with systems with a net
 charge, or where the charge changes such as free energy perturbation, but
 extreme caution is advised when attempting to use PME for these cases. The
 following paper discusses the issues in more detail--
 Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts
 in charged periodic systems via net charge corrections to the ewald potential.
 Journal of Chemical Physics. 1998;108(17):7070-84. <http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1>;
 --
 Rick Venable     5635 FL/T906
 Membrane Biophysics Section
 NIH/NHLBI Lab. of Computational Biology
 Bethesda, MD  20892-9314   U.S.A.
 (301) 496-1905   venabler AT nhlbi*nih*gov
 > From: "Barry Hardy barry.hardy*o*vtxmail.ch"
 <owner-chemistry**ccl.net<mailto:owner-chemistry**ccl.net>>
 Reply-To: CCL Subscribers <chemistry**ccl.net<mailto:chemistry**ccl.net>>
 Date: Sunday, November 4, 2012 6:43 AM
 To: Rick Venable <venabler**nhlbi.nih.gov<mailto:venabler**nhlbi.nih.gov>>
 Subject: CCL: MD simulation of charged systems
 Hi,
 Is there any theoretical or technical objection against running an
 NPgammaT MD simulation on a charged (total charge = -36, due to a
 charged head group in each lipid molecule) membrane model (hydrated bipolar
 monolayer) using PME?
 Many tanks in advance for your input.
 Best,
 Felipe