[gmx-users] Additional repulsive terms for LJ

Timothy Click tclick at nctu.edu.tw
Tue Aug 26 03:55:39 CEST 2014

Thanks for the reply, Justin. I see that the third column is set to 1. Can we add additional terms and set the third column to 2, for instance, if we add a second term? For instance, I may want to keep the original definition from CHARMM for the interaction between LiCL but add a second term, which means that I will want to do the following:

CLA   LIT  1  0.317783572761  0.078240800000
CLA   LIT  2  <sigma>               <epsilon>

I understand the potential ramifications of an ad hoc method, and perhaps I could work on the ion parameters using osmotic pressure calculations as you suggest. For the time being, my postdoc adviser has suggested this method after the fact of suggesting that I alter the charge. I certainly do not wish to return to NAMD, if possible.


柯明 Timothy H. Click, Ph.D.
Department of Biological Science and Technology
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
208 Lab Building 1, 75 Bo-Ai St.
Dong District, Hsinchu, Taiwan 30062
tclick at nctu.edu.tw

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