[gmx-users] golp-CHARMM

Sun Moon sunmoon1360 at yahoo.com
Mon Apr 9 17:20:26 CEST 2018

Hi everyoneI want to simulate carboxylic acid self-assembled monolayer on a goldsurface with Golp-charmm parameters for Au(111) in Aqueous environment.[ref: J. Chem. Theory Comput. 2013, 9, 1616−1630].GolP-CHARMM parameters forthe Au(111) surface are presented in Table 2:

 Surfacea                                AUI                 AUB                  
                                 ε,kJ mol−1 σ, Å                 ε,kJ mol−1 σ, Å
Au−Au                                 0.48 3.80                 0.48 3.80
Au−Au (π-C)                       1.303.20                 0.48 3.80
Au−N(imidazole)                 1.60 2.85                 1.60 2.85
Au−N (unprotonated N termini) 0.902.90             0.90 2.90
Au−S                                      3.20 2.85              3.20 2.85
Au−O                                      0.703.10             0.70 3.10
Au−H                                      0.28 2.70             0.28 2.70
aInteraction strengths ε (kJ mol−1) and distances σ (Å) are given for both surface virtual sites (AUI) and bulk gold atoms (AUB).
--What I am doing is first generating carboxcylic.itp file for carboxylic withSwissparam (for CHARM force field) server and then providing gold.itp file byusing Golp-charm in mentioned paper.I have questions about using these parameters in these paper:1-How to use Epsilon and sigma Au-O in paper for mysimulation? L-J parameters calculate in gromacs with combination rule for intermolecular interaction. 2-Do I extract ebsilon and sigma for oxygen fromthis data with Combination rule? And then use it in non bonding parameter in[atomtype] for oxysion in carboxylic.itp instead of whatever we get withswissparam server?In fact, I don’t know What is the applicationepsilon and sigma Au-X  (X=any atom ) in paper to use in gromacs file? And how to use them in ffnonbonded.itp for charmm27 force field?3-why didn’t author mentioned Au-C in table 2 thispaper?Regards

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