[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.
gmx3 at hotmail.com
Wed Jan 28 10:52:48 CET 2009
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.
Date: Wed, 28 Jan 2009 10:48:57 +0100
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 results.
Sorry, I meant: in double precision
> 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.
> 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,
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