Re: membrane simulation Constraint failure in RATTLE algorithm

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Wed Feb 16 2011 - 22:18:57 CST

Yes, the bilayers were electrically neutral at all times. You can start
with just the bilayers in water. Once you get a stable system you can
remove some of the water and replace with the ions of your choice.
Sometimes with these kinds of simulations you need to run1000-100000
steps with a very small time step (<0.5 fs) to get rid of all the rattle
errors.

Regards,
     Jeff

On 2/16/2011 6:51 PM, snoze pa wrote:
> 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 <mailto: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
> <mailto: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
> ======================================================================
>
>

-- 
======================================================================
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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