Re: [AMBER] setting ionic strength in leap

From: Kris Feher <kris.feher.yahoo.com>
Date: Thu, 12 Jul 2018 18:52:39 +0000 (UTC)

 Dear Tom,thank you for your thoughts. I will try this method too. It seems that issue is not straightforward as I originally thought.Kris



    On Friday, July 6, 2018, 5:51:27 PM GMT+2, Thomas C Bishop <bishop.latech.edu> wrote:
 
 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...

Tom

-- 
    ***********************************
          Thomas C. Bishop
Hazel Stewart Garner Associate Professor
        Chemistry & Physics
          Tel: 318-257-5209
          Fax: 318-257-3823
        www.latech.edu/~bishop
    ***********************************
On 07/05/2018 06:44 PM, Thomas Cheatham wrote:
> printf("\n  %8.3f molecules are necessary to make a molarity of %6.2f
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
  
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jul 12 2018 - 12:00:03 PDT