On Sun, Apr 13, 2014 at 5:39 AM, Sourav Purohit <sour000.gmail.com> wrote:
> Hi ,
>
> I only have counterions in my system and no extra added salt. What value of
> saltcon shall I use? The example in AMBER tutorial also has only
> counterions and a value of 0.1 has been used. Is that the standard value
> to be used?? I find a considerable difference in GB output energies for
> saltcon=0.0 and saltcon=0.1. Kindly guide me on this. I found out the conc.
> of ions in the system in mole/liter and used the value for istrng. Is that
> correct??
>
Are you trying to compare to some type of experiment? The salt
concentration should reflect the conditions in which you are trying to
compute the binding free energy (not necessarily the value you think was
used to model your system in explicit solvent). If you are trying to
compare to experiments done with a 0.1M ionic strength, use 0.1 as istrng
or saltcon.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 13 2014 - 08:30:02 PDT
