Re: [AMBER] setting ionic strength in leap

From: Thomas C Bishop <>
Date: Fri, 6 Jul 2018 10:51:14 -0500

Thanks Tom for the refs and script.

I usually base ion concentration on number waters
(# water in system)*  (desired molarity) / 55.5mol/L
should tell you how many ions to include for a desired concentration.

This of course assumes all waters are behaving as bulk

At the end of the day how much difference is there in these estimates? I
suspect other parts of the simulation are likely more significant...
that differences between the above estimates, e.g. f.f., initial
location of ions/randomization, how much solvent is used, simulation
time etc...


          Thomas C. Bishop
Hazel Stewart Garner Associate Professor
         Chemistry & Physics
          Tel: 318-257-5209
          Fax: 318-257-3823
On 07/05/2018 06:44 PM, Thomas Cheatham wrote:
> printf("\n  %8.3f molecules are necessary to make a molarity of %6.2f
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Received on Fri Jul 06 2018 - 09:00:03 PDT
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