Hello, I have completed a 10ns run. Now I want to extend it to 20ns. The problem is that the initial tpr was compiled for 8 processors and now I have only 4 cores. What I tried to do is used tpbconv to make a 10ns extended tpr, then used an exactly the same mdp file to grompp it all together with -np 4 to a new tpr file. The problem is that at the beginning of the trajectory the structure is undergoing a structural change with 0.12 nm from the initial structure. That means that the structure is actually relaxed and that is not something I want to see. I have used this in my mdp ;------------ VELOCITY INITIATION ----------------------- gen-vel = no gen-temp = 300
That means that no velocities were generated and I expect to see no relaxation but the continuation of my run. What am I doing wrong? How to extend a run without relaxation. Thank you. I appreciate any help. SDA My mdp file is the following. ;-------------PREPROCESSING OPTIONS------------ title = PR "1KLC FREE"; my title cpp = cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-------------RUN CONTROL--------------------- integrator = md; ;--------------OUTPUT CONTROL------------------ ;TRR outpur nstxout = 10000 nstvout = 10000 nstfout = 0 ;LOG and EDR output nstlog = 10000 nstenergy = 10000 ;XTC output nstxtcout = 1000 xtc-precision = 1000 ;-------------START TIME & TIMESTEP----------- tinit = ; [ps] starting time for your run (only makes sense for md, sd, bd integator) dt = 0.005 ; [ps] time step for integration (--"--) nsteps = 1600000 ; (0) maximum number of steps to integrate comm-mode = ; Linear(Remove center of mass translation)/Annular(Remove center of mass ;translation and rotation)/No(no restriction) 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 ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r 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 = 200 (kJ/mol*nm); minimisation is converged when the maximum force is smaller then this value emstep = 0.01; initial step size ;-------------TEMTERAURE CONTROL-------------- tcoupl = berendsen tc-grps = System tau-t = 0.1 ref-t = 300 ;--------- PRESSURE CONTROL--------------------- Pcoupl = no Pcoupltype = Isotropic tau-p = 1 ref_p = 1 compressibility = 4.5E-5 ;------------ VELOCITY INITIATION ----------------------- gen-vel = no gen-temp = 300 ;------------- BONDS ----------------------- constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 8 lincs-warnangle = 30 lincs-iter = 8 morse = no [EMAIL PROTECTED]:~/klc/MD/free> cat pr_free.extendfrom12to20ns.mdp ;-------------PREPROCESSING OPTIONS------------ title = PR "1KLC FREE"; my title cpp = cpp; my C prepocessor (whereIsIt) include = ; dir to include in my topology file define = ; ;-------------RUN CONTROL--------------------- integrator = md; ;--------------OUTPUT CONTROL------------------ ;TRR outpur nstxout = 10000 nstvout = 10000 nstfout = 0 ;LOG and EDR output nstlog = 10000 nstenergy = 10000 ;XTC output nstxtcout = 1000 xtc-precision = 1000 ;-------------START TIME & TIMESTEP----------- tinit = ; [ps] starting time for your run (only makes sense for md, sd, bd integator) dt = 0.005 ; [ps] time step for integration (--"--) nsteps = 1600000 ; (0) maximum number of steps to integrate comm-mode = ; Linear(Remove center of mass translation)/Annular(Remove center of mass ;translation and rotation)/No(no restriction) 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 ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r 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 = 200 (kJ/mol*nm); minimisation is converged when the maximum force is smaller then this value emstep = 0.01; initial step size ;-------------TEMTERAURE CONTROL-------------- tcoupl = berendsen tc-grps = System tau-t = 0.1 ref-t = 300 ;--------- PRESSURE CONTROL--------------------- Pcoupl = no Pcoupltype = Isotropic tau-p = 1 ref_p = 1 compressibility = 4.5E-5 ;------------ VELOCITY INITIATION ----------------------- gen-vel = no gen-temp = 300 ;------------- BONDS ----------------------- constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 8 lincs-warnangle = 30 lincs-iter = 8 morse = no _______________________________________________ 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! 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