[gmx-users] solvation free energy
Hannes Loeffler
Hannes.Loeffler at stfc.ac.uk
Fri Jul 17 12:59:54 CEST 2015
Any particular reason why you want to do it the hard way? I suspect
the answer to this is somewhere in section 5.3 where [pairs_nb] is
discussed. You would have to explicitly set A and B states and not
use couple-*. You may find some old-style input files on
http://www.alchemistry.org/wiki/Main_Page .
On Fri, 17 Jul 2015 12:34:42 +0200
Daniele Veclani <danieleveclani at gmail.com> wrote:
> 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.
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or send a mail to gmx-users-request at gromacs.org.
> >
More information about the gromacs.org_gmx-users
mailing list