Dear all,
In the newest versions of GROMACS the computational electrophysiology
method (CompEL) is implemented through the swapping of solvent molecules
with ions, thus providing a constant transmembrane potential.
However, I am currently employing an implicit solvent model.
My question therefo
Dear all,
I am trying to find the osmotic coefficient of a set of ions in an implicit
solvent system in gromacs 4.5.3. I have found multiple papers reporting an
expression of the form:
Osm. coefficient = 1- (Virial/Ekinetic).
I can find in the manual (appendix B) how the single sum virial is com
Dear all,
I am currently trying to run the computational electrophysiology scheme on
an implicit solvent, coarse-grained system by introducing a little
workaround:
In the manual, it is stated that we can tell the routine what molecules are
'solvent', and what molecules are 'ions' through custom i
Dear all,
I was wondering: what priority does GROMACS use for comparing
[nonbond_params], [pairtypes], and gen-pairs-based cross-terms?
I.e., are pairtypes additive to gen-pairs, with nonbond_params overwriting
any cross-term defined through cross-terms?
The reason I am asking is that I am curre
dear all,
I am employing the computational electrophysiology scheme in gromacs 5.1.4.
I want to set a bulk-offset parameter, such that the scheme only does
position exchanges in a region that is remotely enough from my protein.
However, it seems that I am not able to set the 'bulk-offset' paramet