Dear GMX users, I cannot figure out from the manual whether it is possible to use tabulated non-bonded potentials in a BAR calculation.
I want to estimate the free energy for changing Fe2+ to Fe3+. These have different charges, of course, and also different non-bonded interactions. These non-bonded interactions are neither LJ nor Buckingham, so I am using a lookup table (table_O_Fe2.xvg and table_O_Fe3.xvg) for the "vdw" part (vdw_type=User). I think I should be able to define Fe2 and Fe3 atoms types, and associate the tables (table_O_Fe2.xvg and table_O_Fe3.xvg) with those types in the mdp file: energygrps = O Si Na Ca Al Fe2 Fe3 energygrp_table = O Al O Ca O Fe2 O Fe3 O Na O O O Si Si Al Si Ca Si Fe2 Si Fe3 Si Na Si Si Na Al Na Ca Na Fe2 Na Fe3 Na Na Ca Al Ca Ca Ca Fe2 Ca Fe3 Al Al Al Fe2 Al Fe3 Fe2 Fe2 Fe2 Fe3 Fe3 Fe3 and in the .top file: [ atomtypes ] ;name mass charge ptype A B O 15.99940 -1.20000 A 0.0 0.0 Na 22.99000 0.60000 A 0.0 0.0 Si 28.08000 2.40000 A 0.0 0.0 Ca 40.07800 1.20000 A 0.0 0.0 Al 26.98200 1.80000 A 0.0 0.0 Fe2 55.30500 1.20000 A 0.0 0.0 Fe3 55.30500 1.80000 A 0.0 0.0 [ nonbond_params ] ; i j func C6 C12 O O 1 4.0904959800 2.12268E-09 O Si 1 32.858468400 9.64853E-11 O Na 1 2.2541869930 4.82427E-10 O Ca 1 2.9149186000 4.82427E-10 O Al 1 34.887265640 8.68368E-11 O Fe3 1 40.425524240 1.92800E-10 O Fe2 1 7.542 1.92800E-10 ... Also in the .top file, I define a moleculetype Fe, which is Fe2 in state A and Fe3 in state B: [ moleculetype ] ; name nrexcl Fe 0 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 Fe2 1 Fe Fe 2 1.2 55.3050 Fe3 1.8 55.305 I expect that I could specify this atom in the gro file like this: ... 1764Na Na 1764 3.448 3.335 0.801 0.9202 0.1009 -0.6229 1765Fe Fe 1765 1.123 1.300 0.562 0.3254 -1.0409 -0.6704 1766Ca Ca 1766 2.536 3.320 1.379 -0.5737 -0.4492 -1.8149 ... The problem is that grompp fails, telling me " Fatal error: Group Fe2 not found in indexfile " So, while I want to associate the tables with atom types, it seems GMX is expecting that I am associating the tables (through the energy groups) with a particular atom, which, in my case, moves between two atom types in the BAR calculation. Can anyone tell me whether I am just suffering from a misconception about how the tables (or energy groups) are used, or whether it is in fact just not possible to do BAR (or other free energy) calculations in this way? Thanks Jim Rustad
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