<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>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.</div><div>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.</div><div><br></div><div>Sander</div><div><br></div><br><div><div>On Mar 16, 2010, at 15:00 , sunita gupta wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello All,<br><br>My earlier error ie. dVpot/dlambda values coming zero is solved now....<br>But still two values dEkin/dlambda dG/dl constr as continously coming zero.<br>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?<br>
<br>Any suggestion will be appreciated...<br><br>Below is the .mdp file and a short portion of .log file <br><br>integrator = sd<br>tinit = 0<br>dt = 0.002<br>nsteps = 100<br>
nstcomm = 1<br>nstxout = 100<br>nstvout = 100<br>nstfout = 100<br>nstlog = 500<br>nstenergy = 100<br>nstxtcout = 5000<br>
xtc-precision = 1000<br>nstlist = 10<br>ns_type = grid<br>energygrps = protein sol <1><br>Tcoupl = v-rescale<br>tau_t = 0.1 0.1<br>tc_grps = protein non-protein<br>
ref_t = 300 300<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 173529<br>pbc = xyz<br>rlist = 1.0<br>;domain-decomposition = no<br>coulombtype = pme<br>;rcoulomb-switch = 0<br>
rcoulomb = 1.0<br>epsilon-r = 1<br>vdw-type = cut-off<br>; cut-off lengths =<br>;rvdw-switch = 0.8<br>rvdw = 1.4<br>DispCorr = EnerPres<br>
; Spacing for the PME/PPPM FFT grid =<br>fourierspacing = 0.1<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-06<br>
optimize_fft = yes<br>free_energy = yes<br>init_lambda = 0.1<br>delta_lambda = 0<br>sc_alpha =0.5<br>sc-power =1.0<br>sc-sigma = 0.3<br>
couple-moltype = <1><br>couple-lambda0 = vdw-q<br>couple-lambda1 = none<br>couple-intramol = no<br>constraints = hbonds<br>constraint-algorithm = Lincs<br>unconstrained-start = no<br>
shake-tol = 0.0001<br>lincs-order = 12<br>lincs-warnangle = 30<br><br><b>log file</b><br><br>Long Range LJ corr.: <C6> 3.4799e-04<br>Long Range LJ corr.: Epot -1326.36, Pres: -82.3094, Vir: 1326.36<br>
Energies (kJ/mol)<br> G96Bond G96Angle Proper Dih. Improper Dih. LJ-14<br> 6.99048e+02 1.65819e+03 1.37665e+03 9.23811e+01 8.08449e+02<br> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)<br>
2.87425e+04 2.11542e+05 -2.40740e+03 -1.32636e+03 -7.62482e+05<br> Coul. recip. Potential Kinetic En. Total Energy Temperature<br> -1.12221e+05 -6.33518e+05 1.40404e+05 -4.93114e+05 3.20262e+02<br>
Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd ()<br> 1.22146e+04 -1.29163e+03 0.00000e+00 0.00000e+00 6.13343e-03<br> Cons.2 rmsd ()<br> 6.06182e-03<br><br>DD step 9 load imb.: force 18.9% pme mesh/force 4.177<br>
<br>DD step 99 load imb.: force 21.3% pme mesh/force 2.621<br><br> Step Time Lambda<br> 100 0.20000 0.10000<br><br>Writing checkpoint, step 100 at Tue Mar 16 18:43:50 2010<br>
<br> Energies (kJ/mol)<br> G96Bond G96Angle Proper Dih. Improper Dih. LJ-14<br> 2.87931e+03 4.71650e+03 2.07540e+03 1.47419e+03 8.73118e+02<br> Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb (SR)<br>
2.81990e+04 1.19859e+05 -2.41710e+03 -1.32636e+03 -7.79296e+05<br> Coul. recip. Potential Kinetic En. Total Energy Temperature<br> -1.25837e+05 -7.48800e+05 1.41221e+05 -6.07580e+05 3.22125e+02<br>
Pressure (bar) dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd ()<br> -3.80744e+02 2.05188e+02 0.00000e+00 0.00000e+00 2.31636e-06<br> Cons.2 rmsd ()<br> 2.29249e-06<br> <br>Regards<br>Sunita Gupta<br>
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