[gmx-users] solvation free energy

[Daniele Veclani]

Thank you for your answer.

I read the manual. As I understand it, I should be deleted, from .top file, the
section of non-bonded parameters. It's right?

Of course, after the VdW I'll change the electrostatic transformation.

Best regards
D.V.

2015-07-16 16:55 GMT+02:00 Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>:

> The couple-* parameters take already care of including the non-bonded
> terms internal to your molecule to correctly describe the transfer of M
> to vacuum.  That's the point of those parameters so that you would not
> have to run an additional "correction" in vacuo.  See the discussion in
> the manual (it's section 5.3 for Gromacs 4.6.x).  You would also need to
> compute the electrostatic transformation.
>
> On Thu, 16 Jul 2015 16:26:44 +0200
> Daniele Veclani <danieleveclani at gmail.com> wrote:
>
> > I'm trying to calculate the  solvation free energy of a molecule (M).
> > I have done:
> > M+water ---> dum+water
> >
> > Now I have to do:
> > M(vacuo) --> dum(vacuo)
> >
> > In this case I have a problem, in fact I find a DG = 0.00000 and
> > within the .xvg file there are only zeros.
> >
> > Where is the problem?
> >
> > I use gromacs 5.0.4 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              = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70
> > 0.80 0.90 1.00
> > coul_lambdas             = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> > 0.00 0.00 0.00
> > 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
> >
> > couple-lambda1           = none
> > 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
> >
> > Best regards
> > Daniele Veclani.
>
> --
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