[gmx-users] All-bonds vs h-bonds contraints

Hello Could you please clarify what is the reason for adopting the "all-bonds" constraints as a standard practice in gmx protein simulations? I mean, the argument that "the time step in molecular simulations can be increased by a factor of 4 by replacing the bond vibrations by holonomic constrain

[gmx-users] h-bonds constraints for DPPC sim?

Hi It was mentioned here http://lists.gromacs.org/pipermail/gmx-users/2011-May/061475.html that the constraints option may have to be set to h-bonds to get the exp APL in DPPC equilibration/simulation. Is this indeed true and if so how important is it for membrane/protein simulations? Thanks in

Re: [gmx-users] PRODRG charges

Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case tha

[gmx-users] PRODRG charges

Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? In this case, do we treat all ligand atoms as one charge group? Thanks. George -- gmx-users mailing