VMD-L Mailing List

From: Goldsmith, Jacob (jgoldsmith_at_uky.edu)
Date: Wed Jul 20 2011 - 12:10:28 CDT

How many water molecules do you have in your system? Calculating the number of ions you need for the number of water molecules in your system. This generally works just fine for me.

-Jacob
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Leonardo Trabuco [ltrabuco_at_ks.uiuc.edu]
Sent: Wednesday, July 20, 2011 10:41 AM
To: Edward Lyman
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: autoionize adds too many ions

Hi Ed,

Could you please send me a copy of your system off-list? I'll try to
track down the problem.

Thanks,
Leo

On Fri, Jul 15, 2011 at 9:34 PM, Edward Lyman <edward.lyman_at_gmail.com> wrote:
> Hi all,
>
> I have built a micelle with 100 or so neutral detergent molecules. I
> have checked the charge on each detergent molecule, it is ~10**-16e. I
> built a water box around it, and then tried to use the autoionize
> plugin to add 0.150 mM NaCl. After adding ions, the plugin complained
> that the system has a non integer charge. For some reason 394 Cl ions
> were added, and 27 Na. Any thoughts on what I'm doing wrong? Been
> banging my head on the wall for a day over it...
>
> Best,
> Ed
>
> ps --- I am using vmd 1.9
>
> 

--
Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany
http://www.russelllab.org/people/leo/