[gmx-users] solvation free energy

[hannes.loeffler at stfc.ac.uk]

I do not know how your top file looks like and what you have done to it.

The setup procedure to create the topolog file would be as for a standard MD simulation with M.  You would make sure that the "QUI" label referes to the right indexes in your index file and run TI with you preferred protocol.  This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state.

I suggest to read all parts relating to couple-* in the manual.  This is scattered over several places in the text.

Cheers,
Hannes.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Daniele Veclani [danieleveclani at gmail.com]
Sent: 17 July 2015 08:57
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] solvation free energy

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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