Re: membrane simulation Constraint failure in RATTLE algorithm

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Feb 16 2011 - 17:51:32 CST

Hi Jeffrey,

 Thank you very much for the note and the paper in J. Phys. Chem. B, 2010,
114 (41), pp 13249–13254. Actualy I am trying your system with POPC
membrane.

In page 2, para 2, It is mentioned in your paper that:

"After the 10 ns equilibration period, 13 Ca2+ ions (≈0.1 M) were introduced
into the confined region with 26 Cl- to maintain charge neutrality.
Reference calculations used 13 Na+ and 13 Cl-."

Shall I assume that the membrane was treated neural during equilibration
process. I will re-run the simulation with 1fs time step to check the
problem.

Thank you and Regards
S

On Wed, Feb 16, 2011 at 2:58 PM, Jeffrey Potoff <jpotoff_at_chem1.eng.wayne.edu
> wrote:

> Try running a short simulation with a timestep of 0.5-1.0 fs.
>
>
>
> --
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
>
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
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