After previous discussions that suggested separating vdw and charge mutations, I thought it was literally a 2 stage process. In one stage I modify all charges (including those for disappearing atoms going to zero) from their starting values to their final values, using 10 lambda points and no soft cores. In another stage I modify vdw parameters from their A states to their B states with soft cores, using only the final charge values for A and B states, over 21 lambda points. My statistical error is enormously reduced from when I was trying to modify charges and vdw simultaneously, but the results I'm getting are still a bit puzzling.
It sounds as if I should actually be running 3 series of calculations -- is this correct? I can: 1) Neutralize any atoms which are being disappeared 2) Modify LJ interactions from A state to B state 3) Change charges to final charges for B state. or I can: 1) make the charges of the atoms present in the A-state go to those of the B-state 2) change the LJ of the A-state to the B-state. 3) make the charges of the atoms present in the B-state go to those of the B-state. In the first series of calculations, there is one series of charge mutations that simply changes the charges to 0 on disappearing atoms. The LJ interactions are changed while atoms that will disappear are already set to 0 charge while atoms that do not disappear continue to hold their starting charges. In the final series of calculations, atoms that did not disappear in the B state are changed toward their final charges while the ending state LJ parameters are used. Is this correct? I want to make sure I am not misinterpreting anything. In the second, equivalent series of calculations, the first job is to make all A-state charges go to B-state charges. This would include both atoms that disappear and those that do not disappear but that change parameters. The second job is to change the LJ parameters from A-state to B-state while using... the B-state charges, I presume? I thought that disappearing atoms shouldn't be charged as their LJ parameters change. Under this interpretation, I'm not sure what the 3rd part means. I thought B-state atoms already underwent mutation to B-state charges. Matt Ernst Washington State University _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
