So I've added : --- couple-moltype = Protein couple-intramol = yes --- and now I have non-zero dVcoul/dl, but the dVvdw/dl terms are still zero. Why is this still zero/should I be concerned about that? I'm also happy to no longer be seeing a 100% exchange rate (which I previously forgot to mention was another reason this caught my attention).
---- run_hremd.N.mdp ---- integrator = sd tinit = 0 dt = 0.002 nsteps = 1000000 ; 500000 steps/ns nstxout = 0 nstvout = 0 nstfout = 2500 nstlog = 500 nstenergy = 500 nstdhdl = 100 nstcalcenergy = 50 nstxtcout = 2500 ; 500 steps/ps xtc-precision = 1000 cutoff-scheme = Verlet nstlist = 10 nstcalclr = 1 ns_type = grid pbc = xyz coulombtype = pme rcoulomb = 0.9 fourierspacing = 0.12 pme_order = 4 epsilon-r = 78 vdw-type = cut-off rvdw-switch = 0.7 rvdw = 0.9 constraints = all-bonds constraint_algorithm = lincs gen-vel = yes gen-temp = 300 gen-seed = 47 ref_t = 300 tau_t = 2.00 ; every 2 ps, as suggested when sd used as thermostat tc_grps = system free-energy = yes sc-alpha = 0.5 sc-power = 1 sc-r-power = 6 calc-lambda-neighbors = 1 init-lambda-state = N vdw-lambdas = 0.0 0.0 0.0 0.0 0.1 0.2 0.5 1.0 coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 couple-lambda0 = vdw-q ; all interactions are on at lambda=0 couple-lambda1 = none ; all interaction off at lambda=1 couple-moltype = Protein couple-intramol = yes ---- On Thu, Aug 29, 2013 at 10:55 PM, drew.w.ritchie <drew.w.ritc...@gmail.com>wrote: > Greetings, > > I'm trying to use HREMD on a protein (100 residues) in water to better > sample side chain conformational space in the canonical ensemble. The free > energy part in my 8 .mdp files, with N ranging from 0 to 7, is : > > --- > free-energy = yes > nstdhdl = 100 > init-lambda-state = N > coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 > vdw-lambdas = 0.0 0.0 0.0 0.0 0.1 0.2 0.5 1.0 > sc-alpha = 0.5 > sc-r-power = 6 > couple-lambda0 = vdw-q > couple-lambda1 = none > --- > > My concern is in all of the .log files, I see something like this : > --- > Step Time Lambda > 2000 4.00000 0.00000 > > Energies (kJ/mol) > Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 > 3.07685e+03 4.19165e+03 1.55122e+02 1.74570e+03 2.55986e+02 > LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. > -2.92999e+04 -1.49852e+03 9.25653e+02 -2.04475e+04 1.13608e+05 > Total Energy Temperature Pressure (bar) dVcoul/dl dVvdw/dl > 9.31607e+04 3.02344e+02 2.36558e+03 0.00000e+00 0.00000e+00 > Constr. rmsd Constr.2 rmsd > 2.57681e-05 1.11671e-05 > > Replica exchange at step 2000 time 4 > > Accepted Exchanges: 0 7 5 6 2 3 1 4 > Order After Exchange: 5 2 0 6 7 4 3 1 > --- > > All of the Lambdas are 0 for all of the replicates and all of the dVcoul/dl > and dVvdw/dl are also zero. Does this mean all of my replicates have all > interactions turned on? If so, is it obvious where my mistake is based on > the mdp snippet I've included? > > Thanks, > Andrew Ritchie > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Question-about-HREMD-in-log-file-tp5010835.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- -Andrew Ritchie -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
