Dear gromacs users
In a recent paper I found the following protocol of a gromacs simulation:
"All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the default GROMOS-96 43A1 forcefield [22]. The simulation systems each contained approximately 16,500 Simple Point Charge (SPC) water molecules [23]. Short-range interactions were evaluated using a neighbor list of 1.0 nm updated at every 10 steps. Van der Waals interactions used a cutoff with a smoothing
function such that the interactions slowly decayed to zero between 0.75 nm and 0.90 nm. A long-range analytical dispersion correction was applied to the energy and pressure to account for the truncation of the Lennard-Jones interactions [24]. Electrostatic interactions were evaluated using the particle mesh Ewald (PME) [25] with a real space cutoff of 1.0 nm, a spline order of 6, a Fourier spacing of 0.1 m, and relative tolerance between long and short range energies of . All bonds to hydrogen
were constrained with LINCS [26] with an order of 12, and a time step of 2 fs was used for dynamics."
In the gromacs manual 4.5.4, page 104 it says: "The GROMOS-96 force field was
parameterized with a Lennard-Jones cut-off of 1.4 nm, so be sure to use a Lennard-Jones
cut-off (rvdw) of at least 1.4".
Is it a good idea to set "DispCorr" to "EnerPres" and reduce the rvdw so
dramatically (almost the half value)?
And a second question: Is there a study on the percentage of information
getting lost when reducing the rvdw with and without dispcorr (e.g. to 1.2,
1.0, etc) if the forcefield was parameterized with 1.4?
best,
Bernhard
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