[gmx-users] FEP dEkin/dlambda dG/dl constr. values continuously coming out 0.00000e+00

[Sander Pronk]

Those derivatives should be zero: the kinetic energy is determined by your thermostat and shouldn't change as a function of lambda - as it should for any normal free energy calculation in constant-temperature ensembles.
Also, the constraint energy doesn't change as lambda changes (only the van der Waals and electrostatic energies change in your settings), so that derivative should be zero too.

Sander


On Mar 16, 2010, at 15:00 , sunita gupta wrote:

> Hello All,
> 
> My earlier error ie. dVpot/dlambda values  coming zero is solved now....
> But still two values dEkin/dlambda  dG/dl constr as continously coming zero.
> I understand that for free energy calculation only dVpot/dlambda are required. So, should I ignore these two values and proceed with the work......or due to any mistake with the parameters these values are coming zero and are going to hamper the values of dVpot/dlambda?
> 
> Any suggestion will be appreciated...
> 
> Below is the .mdp file and a short portion of .log file 
> 
> integrator               = sd
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 100
> nstcomm                  = 1
> nstxout                  = 100
> nstvout                  = 100
> nstfout                  = 100
> nstlog                   = 500
> nstenergy                = 100
> nstxtcout                = 5000
> xtc-precision            = 1000
> nstlist                  = 10
> ns_type                  = grid
> energygrps               = protein sol <1>
> Tcoupl = v-rescale
> tau_t = 0.1 0.1
> tc_grps = protein non-protein
> ref_t = 300 300
> gen_vel = yes
> gen_temp  = 300
> gen_seed = 173529
> pbc                      = xyz
> rlist                    = 1.0
> ;domain-decomposition     = no
> coulombtype              = pme
> ;rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> epsilon-r                = 1
> vdw-type                 = cut-off
> ; cut-off lengths        =
> ;rvdw-switch              = 0.8
> rvdw                     = 1.4
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing           = 0.1
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> pme_order                = 6
> ewald_rtol               = 1e-06
> optimize_fft             = yes
> free_energy              = yes
> init_lambda              = 0.1
> delta_lambda             = 0
> sc_alpha                 =0.5
> sc-power                 =1.0
> sc-sigma                 = 0.3
> couple-moltype           = <1>
> couple-lambda0           = vdw-q
> couple-lambda1           = none
> couple-intramol          = no
> constraints              = hbonds
> constraint-algorithm     = Lincs
> unconstrained-start      = no
> shake-tol                = 0.0001
> lincs-order              = 12
> lincs-warnangle          = 30
> 
> log file
> 
> Long Range LJ corr.: <C6> 3.4799e-04
> Long Range LJ corr.: Epot   -1326.36, Pres:   -82.3094, Vir:    1326.36
>    Energies (kJ/mol)
>         G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
>     6.99048e+02    1.65819e+03    1.37665e+03    9.23811e+01    8.08449e+02
>      Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>     2.87425e+04    2.11542e+05   -2.40740e+03   -1.32636e+03   -7.62482e+05
>    Coul. recip.      Potential    Kinetic En.   Total Energy    Temperature
>    -1.12221e+05   -6.33518e+05    1.40404e+05   -4.93114e+05    3.20262e+02
>  Pressure (bar)  dVpot/dlambda  dEkin/dlambda  dG/dl constr.  Cons. rmsd ()
>     1.22146e+04   -1.29163e+03    0.00000e+00    0.00000e+00    6.13343e-03
>  Cons.2 rmsd ()
>     6.06182e-03
> 
> DD  step 9 load imb.: force 18.9%  pme mesh/force 4.177
> 
> DD  step 99 load imb.: force 21.3%  pme mesh/force 2.621
> 
>            Step           Time         Lambda
>             100        0.20000        0.10000
> 
> Writing checkpoint, step 100 at Tue Mar 16 18:43:50 2010
> 
>    Energies (kJ/mol)
>         G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
>     2.87931e+03    4.71650e+03    2.07540e+03    1.47419e+03    8.73118e+02
>      Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb (SR)
>     2.81990e+04    1.19859e+05   -2.41710e+03   -1.32636e+03   -7.79296e+05
>    Coul. recip.      Potential    Kinetic En.   Total Energy    Temperature
>    -1.25837e+05   -7.48800e+05    1.41221e+05   -6.07580e+05    3.22125e+02
>  Pressure (bar)  dVpot/dlambda  dEkin/dlambda  dG/dl constr.  Cons. rmsd ()
>    -3.80744e+02    2.05188e+02    0.00000e+00    0.00000e+00    2.31636e-06
>  Cons.2 rmsd ()
>     2.29249e-06
>  
> Regards
> Sunita Gupta
> -- 
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