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Hi,<br><br>This looks like a bug, unless you have very exotic settings.<br><br>Could you mail me all your input files required to run grompp?<br><br>Berk<br><br><br>> Date: Wed, 28 Jan 2009 13:46:46 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] free_energy = yes & init_lambda = 0.00 does not yield        identical energies to free_energy = no.<br>> <br>> Hi Berk,<br>> <br>> the difference remains when utilizing double precision:<br>> free energy code on with lambda=0.00: Coulomb (SR) = -3.23064e+05<br>> free energy code off: Coulomb (SR) = -3.22653e+05<br>> <br>> Here are the full double precision values:<br>> <br>> ; Free energy control stuff<br>> free_energy = no<br>> <br>> Energies (kJ/mol)<br>> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14<br>> 2.91166e+03 5.90834e+02 1.07820e+03 7.70226e+02 6.22283e+03<br>> LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.<br>> 4.94952e+04 -1.84944e+03 -6.38472e+02 -3.22653e+05 -7.12639e+04<br>> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br>> -3.35336e+05 5.67661e+04 -2.78570e+05 3.00586e+02 6.48848e-01<br>> Cons. rmsd () Cons.2 rmsd ()<br>> 0.00000e+00 0.00000e+00<br>> <br>> <br>> ; Free energy control stuff<br>> free_energy = yes<br>> init_lambda = 0.00<br>> delta_lambda = 0<br>> sc_alpha =0.0<br>> sc-power =1.0<br>> sc-sigma = 0.3<br>> <br>> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14<br>> 2.91166e+03 5.90834e+02 1.07820e+03 7.70226e+02 6.22283e+03<br>> LJ (SR) LJ (LR) Disper. corr. Coulomb (SR) Coul. recip.<br>> 4.94952e+04 -1.84944e+03 -6.38472e+02 -3.23064e+05 -7.12639e+04<br>> Potential Kinetic En. Total Energy Temperature Pressure (bar)<br>> -3.35747e+05 5.67544e+04 -2.78993e+05 3.00524e+02 -4.14918e+01<br>> dVpot/dlambda dEkin/dlambda dG/dl constr. Cons. rmsd () Cons.2 rmsd ()<br>> 1.29815e+03 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00<br>> <br>> I'll try to develop a simplet system to see if this is reproducible <br>> between systems or is system specific.<br>> <br>> I am willing to post my topologies, but what would be most useful at <br>> this point is some assistance confirming if anybody else encounters <br>> this difference.<br>> <br>> Thanks,<br>> Chris.<br>> <br>> --- original message ---<br>> <br>> Hi,<br>> <br>> I would also expect the same results.<br>> I have no clue what kind of system you have.<br>> But check that it is not an accuracy issue.<br>> Could you recalculate the energies in double precision.<br>> <br>> Berk<br>> <br>> > Date: Tue, 27 Jan 2009 20:00:23 -0500<br>> > From: chris.neale at utoronto.ca<br>> > To: gmx-users at gromacs.org<br>> > Subject: [gmx-users] free_energy = yes & init_lambda = 0.00 does not <br>> > yield identical energies to free_energy = no.<br>> ><br>> > Hello,<br>> ><br>> > when applying the free energy code, I expected that the <br>> > instantaneous energy of a given conformation when free_energy = yes <br>> > & init_lambda = 0.00 would be identical to that when free_energy = <br>> > no. However, I have found this not to be the case in zero-step <br>> > mdrun. This is the same result that I get from gmx v 3.3.1, 3.3.3, <br>> > and 4.0.3. Is this expected?<br>> ><br>> > With free_energy = yes & init_lambda = 0.00:<br>> > Coulomb (SR) -3.23064e+05<br>> ><br>> > With free_energy = no:<br>> > Coulomb (SR) -3.22654e+05<br>> ><br>> > and all other energy components are identical. The Coulomb (SR) <br>> > difference seems significant to me. Note that the free_energy = no <br>> > values are identical to those that I get when I use a topology that <br>> > has not been modified to add a B-state so I don't think that my <br>> > A-state values are incorrect.<br>> ><br>> > ## free_energy related .mdp options:<br>> > free_energy = yes<br>> > init_lambda = 0.00<br>> > delta_lambda = 0<br>> > sc_alpha =0.0<br>> > sc-power =1.0<br>> > sc-sigma = 0.3<br>> ><br>> > ## Other .mdp options:<br>> > nsteps = 0<br>> > tinit = 0<br>> > dt = 0.004<br>> > integrator = sd<br>> > comm_mode = linear<br>> > nstcomm = 1<br>> > comm_grps = System<br>> > nstlog = 2500<br>> > nstlist = 5<br>> > ns_type = grid<br>> > pbc = xyz<br>> > coulombtype = PME<br>> > rcoulomb = 0.9<br>> > fourierspacing = 0.12<br>> > pme_order = 4<br>> > vdwtype = cut-off<br>> > rvdw_switch = 0<br>> > rvdw = 1.4<br>> > rlist = 0.9<br>> > DispCorr = EnerPres<br>> > Pcoupl = Berendsen<br>> > pcoupltype = isotropic<br>> > compressibility = 4.5e-5<br>> > ref_p = 1.<br>> > tau_p = 4.0<br>> > tcoupl = Berendsen<br>> > tc_grps = System<br>> > tau_t = 0.1 ref_t = 300. <br>> > annealing = no<br>> > gen_vel = no<br>> > unconstrained-start = yes<br>> > gen_temp = 300.<br>> > gen_seed = 9896<br>> > constraints = all-bonds<br>> > constraint_algorithm= lincs<br>> > lincs-iter = 1<br>> > lincs-order = 6<br>> ><br>> ><br>> > Thank you,<br>> > Chris.<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. 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