Dear gromacs users, Hi, I am trying to pull apart a relatively large protein (CG using the martini force field) by pulling on two groups in opposite directions. To do this, I will be using the following .mdp file. However, I am almost certain that it contains errors:
title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit = 0.0 dt = 0.030 nsteps = 17000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2500 nstvout = 2500 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect the general performance of ; the model. ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; MARTINI - normal temperature and pressure coupling schemes ; can be used. It is recommended to couple individual groups ; in your system seperately. ; Temperature coupling = tcoupl = V-Rescale ; Groups to couple separately = tc-grps = PROTEIN W ; Time constant (ps) and reference temperature (K) = tau_t = 0.3 0.3 ref_t = 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 3.0 compressibility = 3e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 323 gen_seed = 666 ; OPTIONS FOR BONDS = ; MARTINI - for ring systems constraints are defined ; which are best handled using Lincs. constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 60 ; FREEZE GROUP ; Pulling pull = afm pull_geometry = direction pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 2 pull_group0 = pull_group1 = pull pull_vec1 = -0.1764 -0.9823 -0.0625 pull_init1 = -0.1764 -0.9823 -0.0625 pull_rate1 = 0.0001 pull_k1 = 1000 pull_group2 = freeze pull_vec2 = 0.1764 0.9823 0.0625 pull_init2 = 0.1764 0.9823 0.0625 pull_rate2 = 0.0000000001 pull_k2 = 5000 The reason why group 2 has such a high force constant and low pull rate is because I wanted to simulate putting a harmonic constraint on the freeze group. However, when I process this .mdp with grompp, I get the following message: WARNING 1 [file md_vinculin.mdp, line unknown]: Unknown or double left-hand 'pull_group2' in parameter file WARNING 2 [file md_vinculin.mdp, line unknown]: Unknown or double left-hand 'pull_vec2' in parameter file The version of gromacs I have running on my powerpc is 4.0.5 so the pull code should be implemented in the .mdp file. I am not sure if I specified the parameters correctly. Please help! Thanks! --Johnny ------------------------------------------------- Johnny Lam ISPE Berkeley Chapter External Vice President Department of Bioengineering College of Engineering University of California, Berkeley Tel: (408) 655- 6829 Email: john...@berkeley.edu _______________________________________________ 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/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/mailing_lists/users.php