[gmx-users] Free energy of solvation's .mdp of peptide

maggin maggin.chen at gmail.com
Wed May 22 13:14:31 CEST 2013

Hi, if I want to calculate the free energy of solvation of peptide, because
both van der Waals and Coulombic interactions are important for peptide

so I set couple-lambda0 = none  
           couple-lambda1 = vdw-q

is it right?

or it's better to choose wo-stage approach to do this work:

van der Waals coupling:

     sc-alpha          = 0.5     ; use soft-core for LJ (de)coupling
     sc-sigma          = 0.3
     sc-power          = 1
     couple-moltype    = peptide
     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
     sc-sigma          = 0
     couple-moltype    = peptide
     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

Thank you very much!


View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list