[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.
Berk Hess
gmx3 at hotmail.com
Wed Jan 28 20:57:38 CET 2009
Hi,
This looks like a bug, unless you have very exotic settings.
Could you mail me all your input files required to run grompp?
Berk
> Date: Wed, 28 Jan 2009 13:46:46 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.
>
> Hi Berk,
>
> the difference remains when utilizing double precision:
> free energy code on with lambda=0.00: Coulomb (SR) = -3.23064e+05
> free energy code off: Coulomb (SR) = -3.22653e+05
>
> Here are the full double precision values:
>
> ; Free energy control stuff
> free_energy = no
>
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
> 2.91166e+03 5.90834e+02 1.07820e+03 7.70226e+02 6.22283e+03
> LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.
> 4.94952e+04 -1.84944e+03 -6.38472e+02 -3.22653e+05 -7.12639e+04
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -3.35336e+05 5.67661e+04 -2.78570e+05 3.00586e+02 6.48848e-01
> Cons. rmsd () Cons.2 rmsd ()
> 0.00000e+00 0.00000e+00
>
>
> ; Free energy control stuff
> free_energy = yes
> init_lambda = 0.00
> delta_lambda = 0
> sc_alpha =0.0
> sc-power =1.0
> sc-sigma = 0.3
>
> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
> 2.91166e+03 5.90834e+02 1.07820e+03 7.70226e+02 6.22283e+03
> LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.
> 4.94952e+04 -1.84944e+03 -6.38472e+02 -3.23064e+05 -7.12639e+04
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -3.35747e+05 5.67544e+04 -2.78993e+05 3.00524e+02 -4.14918e+01
> dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd () Cons.2 rmsd ()
> 1.29815e+03 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
>
> I'll try to develop a simplet system to see if this is reproducible
> between systems or is system specific.
>
> I am willing to post my topologies, but what would be most useful at
> this point is some assistance confirming if anybody else encounters
> this difference.
>
> Thanks,
> Chris.
>
> --- original message ---
>
> Hi,
>
> I would also expect the same results.
> I have no clue what kind of system you have.
> But check that it is not an accuracy issue.
> Could you recalculate the energies in double precision.
>
> Berk
>
> > Date: Tue, 27 Jan 2009 20:00:23 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] free_energy = yes & init_lambda = 0.00 does not
> > yield identical energies to free_energy = no.
> >
> > Hello,
> >
> > when applying the free energy code, I expected that the
> > instantaneous energy of a given conformation when free_energy = yes
> > & init_lambda = 0.00 would be identical to that when free_energy =
> > no. However, I have found this not to be the case in zero-step
> > mdrun. This is the same result that I get from gmx v 3.3.1, 3.3.3,
> > and 4.0.3. Is this expected?
> >
> > With free_energy = yes & init_lambda = 0.00:
> > Coulomb (SR) -3.23064e+05
> >
> > With free_energy = no:
> > Coulomb (SR) -3.22654e+05
> >
> > and all other energy components are identical. The Coulomb (SR)
> > difference seems significant to me. Note that the free_energy = no
> > values are identical to those that I get when I use a topology that
> > has not been modified to add a B-state so I don't think that my
> > A-state values are incorrect.
> >
> > ## free_energy related .mdp options:
> > free_energy = yes
> > init_lambda = 0.00
> > delta_lambda = 0
> > sc_alpha =0.0
> > sc-power =1.0
> > sc-sigma = 0.3
> >
> > ## Other .mdp options:
> > nsteps = 0
> > tinit = 0
> > dt = 0.004
> > integrator = sd
> > comm_mode = linear
> > nstcomm = 1
> > comm_grps = System
> > nstlog = 2500
> > nstlist = 5
> > ns_type = grid
> > pbc = xyz
> > coulombtype = PME
> > rcoulomb = 0.9
> > fourierspacing = 0.12
> > pme_order = 4
> > vdwtype = cut-off
> > rvdw_switch = 0
> > rvdw = 1.4
> > rlist = 0.9
> > DispCorr = EnerPres
> > Pcoupl = Berendsen
> > pcoupltype = isotropic
> > compressibility = 4.5e-5
> > ref_p = 1.
> > tau_p = 4.0
> > tcoupl = Berendsen
> > tc_grps = System
> > tau_t = 0.1 ref_t = 300.
> > annealing = no
> > gen_vel = no
> > unconstrained-start = yes
> > gen_temp = 300.
> > gen_seed = 9896
> > constraints = all-bonds
> > constraint_algorithm= lincs
> > lincs-iter = 1
> > lincs-order = 6
> >
> >
> > Thank you,
> > Chris.
>
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