Hi,
One needs to be more specific than NB. There is evidence that VDW cutoffs
of traditional lengths cause approximation errors that cause compensating
parameterization errors elsewhere; those effects get worse if the system is
inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that
Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things? We're
not aware of a reason to want to control things manually, but if you have
one, we're keen to hear of it!
Mark
On Wed., 5 Dec. 2018, 09:59 Alex
Dear Gromacs users,
Inverted hexagonal phases are usually simulated (and should be) using a
triclinic box with either semi-isotropic or anisotropic pressure couplings.
I am not sure what a semi-isotropic and anisotropic means in a "Triclinic"
box, exactly?
The .log files look the same for the
Dear Gromacs Users,
I would like to perform umbrella sampling on a protein using RMSD as CV.
RMSD would be measured between the simulated structure and a so called
active conformation and between an inactive conformation. To do that I am
using PLUMED. However, I am new with US simulation and I
