Hello Bharat,
Even though the MD is performed in explicit solvent, the protonation state change attempts are still performed in implicit solvent. Therefore, you still need to set the saltcon to be used in the simulation when GB calculations are to be performed. The saltcon should be the same one used during the fittings of the reference energies for the reference compounds (saltcon=0.1).
I hope this helps,
All the best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Bharat Manna <bharatmanna.gmail.com>
Sent: Monday, July 2, 2018 1:51:09 AM
To: amber.ambermd.org
Subject: [AMBER] Query about Salt-Concentration (soltcon) for Constant pH MD
Dear all,
I'm trying to run constant pH simulation with explicit solvent, following
the Explicit Solvent CpHMD by jswails (
https://urldefense.proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_explicit-2Dsolvent-2Dconstant-2Dph-2Dmd&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=IVlhdkOeZ_TPLAZirxI2WRKcmbwJlX_VRxrurkNh-5w&s=GTAmLolCwA0LVIvBzevfvl-6Q7WKaXSUfTPfKSDlIlU&e=). In the
production run mdin file I can't understand how the saltcon is set to 0.1.
My solvent contains water and ionic liquid mixture. Could you please give
me some advice on how to set the salt concentration?
Thanks
Bharat Manna
PhD Scholar
IIT Kharagpur
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Received on Tue Jul 03 2018 - 07:30:02 PDT
