Dear All Although the tutorials on FE calculations are all excellent and useful, they all appear to involve turning a molecule on or off. As I understand the manual, it is also possible to change one atom into another, i.e. lambda=1 means 100% state A (and 0% state B) and lambda=0 means 100% state B (and 0% state A)
I would assume in this case that "couple-lambda0" and "couple-lambda1" are both set to "vdw-q", in other words, the VDW and coulomb interactions are both "on" for each state? I say this because I am having strange behavior where the VDW terms for state A and state B appear to be added together at lambda=1. In other words, the VDW terms for state A were not turned off at lambda=1. This looks like a bug to me, however, I am too new to GROMACS to be comfortable coming to such a conclusion. I should also mention that I am using user-defined tables for the short-ranged interactions. From the manual, I cannot tell for sure whether such tables are definitely supported in BAR (or, I suppose, in Free Energy calculations in general) I would be grateful for any insight into this problem Jim Rustad -- View this message in context: http://gromacs.5086.n6.nabble.com/Mutating-type-BAR-calculations-tp4997768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
