[gmx-users] FEP dEkin/dlambda dG/dl constr. values continuously coming out 0.00000e+00
sunita gupta
sunita.bio at gmail.com
Tue Mar 16 15:00:07 CET 2010
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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