On 10/28/17 5:49 AM, Archana Sonawani-Jagtap wrote:
Dear all, I have used SPC water model with CHARMM27 forcrfield for performing 100ns protein-DNA simulation instead of TIP3P. I wanted to know if SPC water model can affect my simulation results in anyway considering many charged residues.
Yes, it certainly is. CHARMM specifically balances water interactions assuming CHARMM-modified TIP3P (with LJ on H atoms) to target individual QM water interactions. If you change the water model, you potentially imbalance the entire force field. The water model should generally be viewed as an integral part of the force field, unless one does a complete validation that the change in water model does not negatively impact the target data (water interactions, hydration free energies, helix-coil equilibrium, etc).
CHARMM36 is also superior to CHARMM27 and I recommend you use it instead, particularly if you care about subtle aspects of the DNA structure.
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