Re: [AMBER] adding Na, K and Cl ions matching intracellular conc

From: Matias Machado <>
Date: Wed, 04 Mar 2020 21:23:01 -0300 (UYT)

Dear Vaibhav,

I recommend you to use the SPLIT method, which is described here:

Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

The keyword "saltcon" has nothing to do in explicit solvent MDs.

Best regards,

Matias Machado

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Vaibhav Dixit" <>
Para: "AMBER Mailing List" <>
Enviados: Miércoles, 4 de Marzo 2020 9:49:40
Asunto: [AMBER] adding Na, K and Cl ions matching intracellular conc

Dear All,
I'm interested in understanding if/which Na, K and Cl ions explicitly enter
into the active site of a given protein during MD simulation.
But I can't find a way/trick (from the manual or older posts) to add all
these ions matching the intracellular concentrations and while keeping the
system neutral.
I'm guessing someone in the list must have already done a similar thing.
Thus can someone please suggest me on this aspect.
I'm assuming that if this can be done then I'll have to use saltcon=0 to
avoid GB modelling for salt concentrations.
Looking forward to receiving valuable suggestions from the list.

Thank you and best regards.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
P Please consider the environment before printing this e-mail
AMBER mailing list
AMBER mailing list
Received on Wed Mar 04 2020 - 16:30:03 PST
Custom Search