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DYNGA: a general purpose QM-MM-MD program. I. Application to water |
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| Authors: | CLAUDIA L. PARKER OSCAR N. VENTURA STAN K. BURT RAÚL E. CACHAU |
| Affiliation: | 1. Advanced Biomedical Computer Center , National Cancer Institute-SAIC , Frederick , MD 21701 , USA;2. CCPG, DEQUIFIM, Facultad de Química, UDELAR , Gral. Flores 2124, 11800 , Montevideo , Uruguay;3. Advanced Biomedical Computer Center , National Cancer Institute-SAIC , Frederick , MD 21701 , USA;4. CCPG, DEQUIFIM, Facultad de Química, UDELAR , Gral. Flores 2124, 11800 , Montevideo , Uruguay |
| Abstract: | We present a general purpose QM-MM-MD engine (DYNGA) designed to test alternative hybrid Hamiltonians geared towards the treatment of problems of interest in structural biology including the use of experimental data constraints. In this first presentation we use DYNGA to explore the behaviour of a traditional QM-MM approach in the treatment of the water—water interaction. We find the potential energy hypersurface for the water dimer computed with the HF 4–31G*/TIP3P hybrid Hamiltonian tends to be too flat. We also explore the effect of using traditional QM-MM techniques on proton wires and conclude there is a need for improvement, possibly addressed by using polarizable force fields. |
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