[gmx-users] solvation free energy
Daniele Veclani
danieleveclani at gmail.com
Fri Jul 17 12:34:46 CEST 2015
I read the manual and also some examples of free energy calculation.
when I do the simulation:
M(vacuo) --> nothing(vacuo)
I leave only intramolecular interactions.
How can I just leave these interactions? I don't find the answer in the
manual.
Best regards
D.V.
2015-07-17 10:10 GMT+02:00 <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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