Thanks Erik for your fast response. My reference of Encad FF is<span style="font-style: italic;"> "<span style="font-weight: bold;">Computer Physics Communications 91 (1995) 215-231"; </span></span>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 (<span style="font-weight: bold; font-style: italic;">Biochemistry 2005, 44, 609-616</span>). Using Beeman and other considerations, levitt showed a 2fs can be used without SHAKE. My questions about that are:
<br>
<br>
1. Beeman can be used for integration with encadff, to avoid using SHAKE inside GROMACS?<br>
<br>
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 (<span style="font-weight: bold;">J. Mol. Biol (1983) 168:595-620</span>) but not comparisons with LEAP. Do you have some proper reference?<br>
<br>
3. In pdb2gmx two encadff are available. Which is the one described in Levitt1995??<br>
<br>
4. In levitt1995, a <span style="font-weight: bold;">Asc</span> scaling factor is applied to repulsive LJ potential in order to compensate loss of dispersive interactions due to cutoff. Does <span style="font-weight: bold; font-style: italic;">
encadshift </span>uses
that scaling?? If that is the case, Is required to define it
explicitly, or the program decides based on encadshift value???<br>
<br>
5. Can encadshift be used with OPLS, with short cutoffs???<br>
<br>
Thanks in advance<br>
<br>
Leonardo<br><br>~~~~~~~~~~~~~~~~~~~~~~~~~
<br>Leonardo Andres Sepúlveda Durán<br>Biochemist<br>Universidad de Chile<br>Codigo postal: 752-0249<br>~~~~~~~~~~~~~~~~~~~~~~~~~