Dear All,
In my MD simulation I only added counter ions (20 Na+ ions) to neutralize the system. Now I want to do MM_PBSA calculations for my MD runs using g_mmpbsa. In order to do perform polar solvation energy, I have to define parameters pcon and ncon.
According to my system what values should be assigned to those two parameters? If I assign 0 (zero) value for both parameters, is it correct or can I assign pcon and ncon as 0.150 ?
I don't have clear solution for this problem. Please can anyone help me?
Thank you in advance.
The pcon and ncon values of 0.150 M assume the "physiological" ionic strength.
Hence, if you want to use the value of 0.150 M, you will need to have one sodium and one chloride ion per every ~370 water molecules in your system (on top of the sodium ions included to neutralize the negative charge of the system).
Otherwise, use pcon=0 and ncon=0.
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http://pubs.acs.org/doi/abs/10.1021/ci500020m
". . . The net charge on the system was then neutralized by adding counterions as required. The ionic strength was adjusted by the addition of 0.150 M of NaCl . . ."
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