[gmx-users] CompEL bulk offset parameter unavailable in gromacs 5.1.4?

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'

[gmx-users] Order in which gromacs calculates non-bonded parameters

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

[gmx-users] Computational electrophysiology, implicit solvent and coarse-grained system: atom/molecule definitions?

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

[gmx-users] Calculating osmotic coefficient through virial/kinetic terms: what is the handy way?

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

[gmx-users] Computational Electrophysiology: how about implicit solvent?

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