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Joined: Nov 2005
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Joined: Nov 2005
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I aware that most Charmm molecules such as proteins and lipids were fitted based on the CHARMM-modified TIP3P water model.

Is there any harm if I were to use the original TIP3P or indeed any other 'standard' water models such as SPC and SPC/E to run a CHARMM simulation?

Has anyone carried out some evaluative work regarding the outcome of, say protein structures, when different water models were used?

Thanks in advance for any comment.

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The original TIP3P has virtually identical properties as the modfiied TIP3P. Probably no great harm using other water model, not necessarily much gain either.
Some references:
Mark, P., and Nilsson, L. (2001). Molecular Dynamics of the Ala-Pro Dipetide in Water. Conformational Dynamics of Cis- and Trans Isomers Using Different Water Models. J Phys Chem B 105, 8028-8035.
Mark, P., and Nilsson, L. (2002). A Molecular Dynamics Study of Tryptophan in Water. J Phys Chem B 106, 9440-9445.
Mark, P., and Nilsson, L. (2002). Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. J Comp Chem 23, 1211-1219.
Glass, D.C., Krishnan, M., Nutt, D.R., and Smith, J.C. (2010). Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models. Journal of Chemical Theory and Computation 6, 1390-1400.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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