I am simulating a system in N,N-dimethylacetamide (DMA) and ions (Li+ and Cl-) using CHARMM36. However, I have found that the ions tend to cluster together because of the lower dielectric constant of DMA.If I lower the formal charges (+/-0.5), the clustering diminishes considerably. A former postdoc in the group had used NAMD when simulating a similar system and simply added an additional repulsive term to the Li-Cl LJ interactions to remove the clustering. Before I attempt anything, I wanted to ask if this is possible in Gromacs by adjusting parameters in the [pairwise] section of the ffnonbonded.itp. Or, is the adjustment of the formal charge an acceptable physical representation because of the difference in solvents (water for the CHARMM36 parameters of LiCl vs. DMA with LiCl)?
Thanks. Cordially, 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 (R.O.C.) tcl...@nctu.edu.tw -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
