[gmx-users] Another questions about Encad inside GROMACS
lindahl at sbc.su.se
Tue Oct 18 20:06:49 CEST 2005
On Oct 18, 2005, at 6:21 PM, Leonardo Sepulveda Durán wrote:
> 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 inside GROMACS?
No. Your best bet for long timesteps in general is to use LINCS,
possibly in combination with dummy hydrogens.
> 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?
All verlet class integrators yield the same trajectory, but the
velocity accuracy depends on how you do the averaging.
> 3. In pdb2gmx two encadff are available. Which is the one
> described in Levitt1995??
"s" is the solvent one, "v" the vacuum version (scaled down charges).
> 4. In levitt1995, a Asc scaling factor is applied to repulsive LJ
> potential in order to compensate loss of dispersive interactions
> due to cutoff. Does encadshift uses that scaling?? If that is the
> case, Is required to define it explicitly, or the program decides
> based on encadshift value???
You can use true integrated dispersion corrections in Gromacs.
I would not recommend Encad for accurate solvent simulations at this
point - the primary use is the vacuum version for rapid
discrimination. Some trials we've done indicate that OPLS-AA/L
combined with TIP4p produce cRMS values for some small test proteins
around 1.1-1.2A, while Encad & F3C gives >=2A.
Erik Lindahl <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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