Hello, I am trying to run two step energy minimization with steep followed by cg on a structure with hydrogen vsites and heavyh (in OPLSAA). In gromacs 3.3.3 I had an error in grompp when starting cg - it reported that cg was incompatible with constraint bonds (LINCS was off, I guess it was about dummy sites). Not in 4.0.2 I receive an error from mdrun - system explodes complaining about deviation in bond length after LINCS, though it is off.
Two questions: 1/ Can I use cg with dummies? 2/ It there any (scientific) advantage of using steep+cg except for speed? Thanks Steep and CG mdp files are below ======================================================================= ;-------------PREPROCESSING OPTIONS------------ title = "Energy minimization" cpp = /usr/bin/cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-------------RUN CONTROL--------------------- integrator = steep; ;-------------START TIME & TIMESTEP----------- nsteps = 5000 ; (0) maximum number of steps to integrate nstcomm = 1 ;-------------NEIGHBOR SEACHING--------------- nstlist = 5; frequency o update neighbor list ns_type = grid; make a gid in the box and check only ;neighboring grid cell when constructing a new neighbor list rlist = 1.0; cut-off distance for the short-range neighbor list ;-------------ELECTROSTATICS------------------ coulombtype = Reaction-field ; reaction field with coulomb cut-off rcoulomb rcoulomb = 1.5 ;distance for the coulomb cut-off epsilon_rf = 80;dielectric constant epsilon_r = 1; vdwtype = cut-off; twin-range cut-off`s with neighbor list cut-off rlist ;and VdW cut-off rvdw, where rvdw>rlist rvdw = 1.0 ; distance for for the LJ or Buckingam cut-off ;-------------ENERGY MINIMIZATION------------- emtol = 500 (kJ/mol*nm); minimisation is converged when the maximum force is smaller then this value emstep = 0.01; initial step size ;-------------TEMTERAURE CONTROL-------------- tcoupl = v-rescale tc-grps = System tau-t = 0.1 ref-t = 0 ld_seed = 24564314 ;--------- PRESSURE CONTROL--------------------- Pcoupl = no Pcoupltype = Isotropic tau-p = 1 ref_p = 1 compressibility = 4.5E-5 ;------------ VELOCITY INITIATION ----------------------- gen-vel = no gen-temp = 0 ;------------- BONDS ----------------------- constraints = none constraint-algorithm = Lincs unconstrained-start = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 8 lincs-warnangle = 30 lincs-iter = 8 ============================================================================ ;-------------PREPROCESSING OPTIONS------------ title = "Energy minimization" cpp = /usr/bin/cpp; my C prepocessor (whereIsIt) ;-------------RUN CONTROL--------------------- integrator = cg; ;-------------START TIME & TIMESTEP----------- nsteps = 5000 ; (0) maximum number of steps to integrate nstcomm = 1 ;-------------NEIGHBOR SEACHING--------------- nstlist = 5; frequency o update neighbor list ns_type = grid; make a gid in the box and check only ;neighboring grid cell when constructing a new neighbor list rlist = 1.0; cut-off distance for the short-range neighbor list ;-------------ELECTROSTATICS------------------ coulombtype = Reaction-field ; reaction field with coulomb cut-off rcoulomb rcoulomb = 1.5 ;distance for the coulomb cut-off epsilon_rf = 80;dielectric constant epsilon_r = 1; vdwtype = cut-off; twin-range cut-off`s with neighbor list cut-off rlist ;and VdW cut-off rvdw, where rvdw>rlist rvdw = 1.0 ; distance for for the LJ or Buckingam cut-off ;-------------ENERGY MINIMIZATION------------- emtol = 100 (kJ/mol*nm); minimisation is converged when the maximum force is smaller then this value emstep = 0.01; initial step size nstcgsteep = 1000 ;-------------TEMTERAURE CONTROL-------------- tcoupl = v-rescale tc-grps = System tau-t = 0.1 ref-t = 0 ld_seed = 24564314 ;--------- PRESSURE CONTROL--------------------- Pcoupl = no Pcoupltype = Isotropic tau-p = 1 ref_p = 1 compressibility = 4.5E-5 ;------------ VELOCITY INITIATION ----------------------- gen-vel = no gen-temp = 0 ;------------- BONDS ----------------------- constraints = none constraint-algorithm = Lincs unconstrained-start = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 8 lincs-warnangle = 30 lincs-iter = 8 morse = yes _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
