[gmx-users] spatial distribution function in a binary solvent mixture

Dear all, I'm working with a binary solvent mixture containing 2000 molecules (1800 type-A + 200 type-B). Both the types of solvent molecules have similar structure (they are both diatomic molecules) except the polarity.I'm trying to calculate sdf of type-B solvent molecules. I followed the

Re: [gmx-users] spatial distribution function in a binary solvent mixture

Thanks Chris. I presume g_sdf won't be helpful for my system. > I think that you have a misconception about what g_spatial does. For a > system with many type A and many type B, you need to average over all > of one type as the central solute to compute an rdf, and perhaps that > is what you wan

[gmx-users] Problem in Energy minimisation for a rigid body system

Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupied by the metal atom and four

Re: [gmx-users] Problem in Energy minimisation for a rigid body system

Hi Mark, Initially I included all the sets of bonds (as you have mentioned). Then I get the warning message while doing grompp, which says number of constraints is more (18 as I've defined) than required (it shouldn't be more than 15). With all the sets of bonds defined also, energy minimization d