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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 results.<br><br>Berk<br><br>> Date: Tue, 27 Jan 2009 20:00:23 -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>> Hello,<br>> <br>> when applying the free energy code, I expected that the instantaneous <br>> energy of a given conformation when free_energy = yes & init_lambda = <br>> 0.00 would be identical to that when free_energy = no. However, I have <br>> found this not to be the case in zero-step mdrun. This is the same <br>> result that I get from gmx v 3.3.1, 3.3.3, 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 has <br>> not been modified to add a B-state so I don't think that my A-state <br>> 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 <br>> 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>> 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. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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