Hi, I have a system in a slab geometry. A surface exists at z = 0; many hydrogens protrude from the surface, and these hydrogens are mostly (but not precisely) immobile. Above the surface, there is liquid, including the anion BF4- (tetrahedral arrangement of fluorines around a central boron). The liquid region is large, extending far from the surface, (far above the surface, the liquid behaves like liquid in the bulk).
There is hydrogen-like bonding between the hydrogens protruding from the surface and the fluorines in BF4-. I would like to calculate the "average" H-F distance, where H atoms protrude from the stationary surface and F atoms exist on the BF4- ions. But saying that I want to compute the "average" H-F distance is very vague. I can think of at least two possible, hopefully reasonable, ways to formulate the problem: (i) For the purpose of calculating the average H-F separation, only consider fluorines on BF4- ions which are within a certain perpendicular distance z0 from the surface. In other words, consider the BF4- ions which lie in the region 0 < z < z0 (where z0 is positive and very small compared to the z dimension of the simulation box). Then, using those BF4- ions, I calculate the (time-averaged) H-F separation. (ii) For the purpose of calculating the average H-F separation, only consider fluorines when they are a certain small distance from any hydrogen. Are (i) or (ii) these feasible? For (i), I can think about using g_select to select BF4- ions which are a distance of z0 or less from the surface at z = 0. Maybe I would use a selection like 'res_com of resname BF4 and z < 10' (where z0 = 10). The problem with this is that, I think, I would obtain an index file for each simulation timestep. So, I guess then if I have 200,000 simulation timesteps, I would have to run g_bond 200,000 times! (Or would g_dist be appropriate here?) Also, even my formulation in (i) is a little awkward; fluorines at one edge of the xy dimension would be far from hydrogens immobilized at the other side of the xy dimension, so I would get artifacts. For (ii), it seems that g_hbond might be useful. However, it does not seem that fluorine is currently implemented as a hydrogen bond acceptor for use in g_hbond. I have never attempted to modify the Gromacs code and I am not sure how easy this would be. But if H-F is a hydrogen-like bond, then (average) H-F bond length is what I am going after, I guess. Do you know of any recipes with which to do this, or do you have any suggestions? Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists