From: Brian Radak (bradak_at_anl.gov)
Date: Tue Apr 18 2017 - 16:56:02 CDT
Most NAMD users make use of the latest CHARMM force field (currently
C36). These force fields have always, to my knowledge, been
parameterized with the modified TIP3P potential which adds Lennard-Jones
centers to the hydrogen atoms. This is not the same thing as TIP3P,
although some reports in the literature equate the two. The standard
TIP4P and TIP5P potentials are not widely used in biomolecular
simulations. Some users occasionally use the TIP4P-Ew
re-parameterization (usually with the AMBER force field).
Ultimately the choice of solvent model is independent of NAMD - it can
generally handle all of them. It all depends on what force field
combination you think is most useful.
On 04/18/2017 04:05 PM, Oscar Bastidas wrote:
> Would someone please tell me if TIP3P water molecules are the standard
> solvation for the version of NAMD presently available? I've heard of
> so-called TIP4P and TIP5P but I wasn't sure if these were special
> solvation models. Thank you.
> Respectfully submitted,
> Oscar B.
> Oscar Bastidas, Graduate Student
> Department of Chemical and Life Science Engineering
> Virginia Commonwealth University
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
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