[gmx-users] Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR

Sonia Milena Aguilera Segura sm.aguilera37 at uniandes.edu.co
Mon Sep 17 04:45:38 CEST 2012


I'm preparing my mdp and topology files for running free energy calculations using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can find it here http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html). According to this tutorial, the simultaneous coupling of both Coulombic and van der Waals terms leads to instability. So, it is usefull to prepare the mdp files as follows (off course including all other parameters):

van der Waals coupling:

     sc-alpha          = 0.5     ; use soft-core for LJ (de)coupling
     sc-sigma          = 0.3
     sc-power          = 1
     couple-moltype    = LIG
     couple-intramol   = no
     couple-lambda0    = none    ; non-interacting dummy in state A
     couple-lambda1    = vdw     ; only vdW terms on in state B

Coulombic coupling:

     sc-alpha          = 0       ; soft-core during (dis)charging can be unstable!
     sc-sigma          = 0
     couple-moltype    = LIG
     couple-intramol   = no
     couple-lambda0    = vdw     ; only vdW terms in state A (the previous state B is now A)
     couple-lambda1    = vdw-q   ; all nonbonded interactions are on in state B

However, I don't understand how can this leads to a fully interacting molecule if all the charges in the topology file have been set to zero. Does it mean that for the second calculation (coulombic coupling) I have to use the original topology file with all charges? Or, should I use the same topology with zero charges?

Thanks in advance,

Sonia Aguilera
Graduate student-Chemical Engineering Department
Universidad de los Andes

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