Dear Fulbabu Sk,
Check the help/manual for keyword "addIonsRand" and read the following papers:
Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations
https://doi.org/10.1021/acs.jctc.9b00953
SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation
https://doi.org/10.1021/acs.jctc.7b01254
Best,
Matias Machado
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Fulbabu Sk" <phd1701171005.iiti.ac.in>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 27 de Agosto 2020 9:55:29
Asunto: [AMBER] Help for building two different salt concentration system using tLeap module
Hi, guys,
I would like to do the simulation of a protein-protein-ligand system at two
different salt-concentrations (although, I don't know the default salt
concentration of the leap module of amber). Is there any tutorial available
in AMBER?
Any suggestions in this regard would be deeply appreciated.
--
Stay at Home, Stay Safe!
Thanks and best regards,
*****************************
*Md Fulbabu Sk*
*BSBE, IIT Indore, India *
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Received on Thu Aug 27 2020 - 08:00:02 PDT
