[gmx-users] Another questions about Encad inside GROMACS
Leonardo Sepulveda Durán
leonardosepulveda at gmail.com
Tue Oct 18 18:21:22 CEST 2005
Thanks Erik for your fast response. My reference of Encad FF is "Computer
Physics Communications 91 (1995) 215-231"; i have some questions about that.
First, levitt used a Brook's modification of Beeman's algorithm to mantain
energy. I have read from daggett's works this method is very conservative,
better than normal CHARMM shift function, and very similar to FSHIFT, using
only cutoff without PME for electrostatics (Biochemistry 2005, 44, 609-616).
Using Beeman and other considerations, levitt showed a 2fs can be used
without SHAKE. My questions about that are:
1. Beeman can be used for integration with encadff, to avoid using SHAKE
2. Which is better for energy conservation? Leap frog (Which is the default
GROMACS integrator, isn't?) Velocity verlet, verlet or Beeman? I found a
reference about VER and SHAKED VER (J. Mol. Biol (1983) 168:595-620) but not
comparisons with LEAP. Do you have some proper reference?
3. In pdb2gmx two encadff are available. Which is the one described in
4. In levitt1995, a Asc scaling factor is applied to repulsive LJ potential
in order to compensate loss of dispersive interactions due to cutoff.
uses that scaling?? If that is the case, Is required to define it
explicitly, or the program decides based on encadshift value???
5. Can encadshift be used with OPLS, with short cutoffs???
Thanks in advance
Leonardo Andres Sepúlveda Durán
Universidad de Chile
Codigo postal: 752-0249
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