[gmx-users] solvation free energy, electrostatic transformation

[Hannes Loeffler]

What happens when you do both transformations simultaneously, i.e.
sc-coul=yes?


On Mon, 27 Jul 2015 15:55:04 +0200
Daniele Veclani <danieleveclani at gmail.com> wrote:

> I'm trying to calculate the  solvation free energy of a molecule (M).
> 
> I have done a VdW.  transformation.
> 
> I have done also a  electrostatic transformation. But I get an
> incorrect value (large overestimation of DG solvation).
> 
> I use gromacs 5.0.4 with gromos 54a7 force fields and my .mdp file
> (for lambda 00) is:
> integrator               = sd
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 2500000
> comm_mode                = angular
> nstcomm                  = 100
> nstxout                  = 500
> nstvout                  = 500
> nstfout                  = 0
> nstlog                   = 500
> nstenergy                = 500
> nstxout-compressed       = 0
> cutoff-scheme            = group
> nstlist                  = 0
> ns_type                  = simple
> pbc                      = no
> rlist                    = 0
> coulombtype              = cutoff
> rcoulomb                 = 0
> epsilon_r                = 1
> vdwtype                  = cutoff
> rvdw                     = 0
> DispCorr                  = no
> fourierspacing           = 0.12
> pme_order                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> tcoupl                   = berendsen
> tc_grps                  = system
> tau_t                    = 0.1
> ref_t                    = 300
> Pcoupl                   = no
> tau_p                    = 1.0
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> free_energy              = yes
> init_lambda_state        = 0
> delta_lambda             = 0
> calc_lambda_neighbors    = 1
> vdw_lambdas              = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
> 1.00 1.00 1.00
> coul_lambdas             = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70
> 0.80 0.90 1.00
> bonded_lambdas           = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00
> restraint_lambdas        = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00
> mass_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00
> temperature_lambdas      = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00
> sc-alpha                 = 0.5
> sc-coul                  = no
> sc-power                 = 1.0
> sc-sigma                 = 0.3
> couple-moltype           = QUI
> couple-lambda0           = vdw-q
> 
> couple-lambda1           = vdw
> couple-intramol          = no
> nstdhdl                  = 10
> gen_vel                  = no
> constraints              = all-bonds  ; we only have C-H bonds here
> constraint-algorithm     = lincs
> continuation             = no
> lincs-order              = 12
> 
> 
> What's wrong?
> 
> Best regards
> D.V.