[gmx-users] free_energy = yes & init_lambda = 0.00 does not yield identical energies to free_energy = no.

[Berk Hess]

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








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 results.

Sorry, I meant: 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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