VMD-L Mailing List

From: sting (stg1979_at_126.com)
Date: Mon May 13 2019 - 07:37:46 CDT

Thank you Kelly! I will try it.

Best regards
Sting

At 2019-05-10 12:44:19, "McGuire, Kelly" <mcg05004_at_byui.edu> wrote:

You could try using CHARMM GUI multicomponent assembler. I used it to make a water/ethanol solvent mixture for a simulation.

http://www.charmm-gui.org/?doc=input/multicomp

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of sting <stg1979_at_126.com>
Sent: Thursday, May 9, 2019 8:22 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: How to add ions to a system with non-water solvents
 
Dear All,

     I construct a simulation system with formic acid as solvent, and want to ionize this system. I noticed that the VMD plugin Autoionize can only replace water molecules with ion molecules. Is there any other way to ionize my system ? Many thanks for any suggestion !

Best regards
Sting