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’m calling the ferrous iron “Mg” for convenience Here are the relevant fragments of my current 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 Mg 55.30500 1.20000 A 0.0 0.0 Fe 55.30500 1.80000 A 0.0 0.0 ;(The tables “table_O_Fe.xvg” and “table_O_Mg.xvg” exist and are read in without problems) [ nonbond_params ] ; these now give the multipliers for the tables columns ; 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 Mg 1 7.542 1.92800E-10 O Fe 1 40.425524240 1.92800E-10 ------------ . . . Now I have defined a molecule type for the changing ion labeled “Cr” in the .gro file, which transforms from atom type Mg to atom type Fe [ moleculetype ] ; name nrexcl Cr 0 [ atoms ] ; nr type resnr residue atom cgnr charge mass TypeB ChargeB MassB 1 Mg 1 Mg Mg 2 1.2 55.3050 Fe 1.8 55.305 . . . And the relevant portion of my .mdp file for lambda=0 coulombtype = PME-Switch rcoulomb = 1.0 vdw_type = User . . . free-energy = yes couple-moltype = Cr init-lambda = 0.0 foreign-lambda = 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 couple-lambda0 = vdw-q couple-lambda1 = vdw-q It runs fine, but when I look at the RDF for the changing ion (Cr), it does not go smoothly between Mg and Fe as lambda goes from 0 to 1, but, at lambda=1, the peak position is pushed way further out than either Mg (~0.2 nm) and Fe (~0.19 nm) (it’s not an aqueous system b.t.w.) and sits at 0.23 nm or more. At lambda=0, everything looks OK (i.e. the "Cr" ion gives the same g(r) as the "Mg" ion) So it makes me wonder if the short-ranged interactions in the tables are simply being added together without regard for what the lambda value is? (i.e. at lambda =1, we still get the entire short range interaction for the "A" state added to that of the "B" state). Is it possible that there is a bug in the integration of non-bonded tables into the free energy capability? Or do I misunderstand how the lambda is applied in this "mutating" type free energy problem? Thanks for all the help already, and for any further insight anyone can provide. I can show a picture if the RDFs if you want to see them. James R. Rustad, Ph.D. Research Associate, Corning, Inc. Professor Emeritus, UC Davis Corning Incorporated One Science Center Drive SP TD 01-1 Corning, NY 14831 -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-and-non-bonded-tables-revisited-tp4997686.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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