VMD-L Mailing List

From: bo liu (liubo.njuer_at_gmail.com)
Date: Wed Nov 19 2008 - 08:42:58 CST

Hi Gumbart,

you mean that if i want to keep the ion concentration of my system at 0.15M,
what i have to do is to set it as 0.30M with autonionize?

Bo

2008/11/19 JC Gumbart <gumbart_at_ks.uiuc.edu>

> The value given is just an example, you should take it with a grain of
> salt. (hahaha) There is not a default value; you either must give a
> concentration or a fixed number of ions.
>
>
>
> The autoionize gui plugin has an option to only neutralize the system;
> alternatively, you could just specify ¨Cis .0001 to make it only place enough
> ions to neutralize the system and no more (assuming this is what you want to
> do). Physiological concentrations are definitely higher than 50 mM, more
> like 150 mM, I think, although the relevant ion species and concentrations
> vary so consider the native environment of your system carefully. Keep in
> mind though that the concentration in the autoionize plugin is effectively
> twice that in experiments (i.e. 150mM KCl in experiment -> 300mM total ion
> concentration (K+ and Cl-) in autoionize).
>
>
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Rabab Toubar
> *Sent:* Tuesday, November 18, 2008 7:40 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Autoionize plugin
>
>
>
> Hi all,
>
>
>
> 1- I was wondering what is the importanced of the ionic concentration in
> the mentioned script at this webpage:
> http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/
>
>
>
> autoionize -psf file.psf -pdb file.pdb -is 0.05
>
>
>
> Is it to resemble the physiological pH? What if I didn't include it in the
> script, is there a default value for it?
>
>
>
> 2- Which would be more accurate: calculating the net charge on the peptide
> and specifying the number of opposiite charge to neutralize it - provided it
> is reasonably small, or using the autoionize
>
>
>
> Thanks
>
> Rabab
>
>
> 

-- 
-Bo Liu
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Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
College of Chemistry and Chemical Engineering, Graduate University of
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