Hi again,
I am trying to pull apart a CG protein (to verify CG results with those of already published works using atomistic MD). Using the previous suggestions, my new pull code is the following: title = Martini cpp = /usr/bin/cpp integrator = md ; start time and timestep in ps tinit = 0.0 dt = 0.030 nsteps = 2500 ; 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 = 33 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 = ; 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 ; 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 ; 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 constraints = none ; Type of constraint algorithm = constraint_algorithm = SHAKE ; 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 ; freezegrps = freeze ; freezedim = Y Y Y ; Pulling pull = umbrella pull_geometry = distance pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = freeze pull_group1 = pull pull_init1 = 0.0 0.0 0.0 pull_rate1 = 5000.0 pull_k1 = 100 The reason why the number of time steps is quite small, the pull_rate quite high, and the force constant low is because I wanted to verify that the code actually works before doing the actual production run (around 13 ns). The issue I'm running into is that when I check the results using VMD, it seems almost as if the simulation ignored all of my pull commands. I changed the rate, force constant, and the # timesteps to many different values but to no avail. Every result seems to indicate that my pull commands were not read (nothing happens aside from vibration). I highly doubt that there is a bug (as mentioned in an earlier post). I don't know why this is happening. Is there something wrong with the code? I really appreciate the help! --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
