[gmx-users] "Mutating" type BAR calculations

Dear All Although the tutorials on FE calculations are all excellent and useful, they all appear to involve turning a molecule on or off. As I understand the manual, it is also possible to change one atom into another, i.e. lambda=1 means 100% state A (and 0% state B) and lambda=0 means 100% stat

[gmx-users] BAR and non-bonded tables revisited

All Thanks much for your previous help. I now have the calculation running. However I get suspicious results that make me think that BAR may not be integrated with tables correctly. In this problem I am trying to change an Mg ion into an Fe ion (really its a ferrous iron to a ferric iron, but I’

[gmx-users] Re: Gromacs files to simulate SiO2 film

Alexey I have a quartz(101) surface and a gromacs BKS input file that might get you started at least. Cheers Jim -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-files-to-simulate-SiO2-film-tp4997666p4997673.html Sent from the GROMACS Users Forum mailing list archive at

[gmx-users] Re: Gromacs files to simulate SiO2 film

Dear Alexey, The answer to this question partly depends on your application- for example, is it important for the surface of the amorphous SiO2 to be able to undergo reactions like Si-O-Si + H2O = 2SiOH? Regards, Jim Rustad -- View this message in context: http://gromacs.5086.n6.nabble.com/Grom

[gmx-users] Re: BAR calculations with tabulated non-bonded potentials

Justin A. Lemkul wrote > > > You don't need the pull code if the two atoms are in the same > [moleculetype] - a > "molecule" in Gromacs is any set of atoms; they don't necessarily have to > make > chemical sense. The only problem I see is that if you have two atoms in > the > same location,

[gmx-users] Re: BAR calculations with tabulated non-bonded potentials

Justin A. Lemkul wrote > > I don't know how complex the system is you're dealing with, but at this > point, > isn't it just far more straightforward to construct a rudimentary force > field > with a few atom types rather than rely on (slow) tabulated functions and > potential funny business to

[gmx-users] Re: BAR calculations with tabulated non-bonded potentials

Thanks- yes, I suspected this might be the case, however, in the context of a free energy calculation it seems difficult to associate the lookup table with a molecule type rather than an atom type. In other words, I have defined a molecule "Fe" which will change from Fe2 to Fe3. So, its true th