2009/9/8 Mark Abraham <mark.abra...@anu.edu.au> > Jennifer Williams wrote: > >> Hi users, >> >> I am running a very simple simulation of methane inside a pore (v.much >> like a carbon nanotube but in my case the tube is supposed to represent >> silica.) I keep this tube frozen. >> >> I start with an energy minimisation-however this runs to completion almost >> instantly and I keep get NaN for my potential energy: >> >> Steepest Descents converged to machine precision in 18 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = nan >> Maximum force = 6.5738518e+01 on atom 2133 >> Norm of force = 1.5461593e+00 >> > > This nan suggests some kind of severe atomic overlap. Reconsider your > coordinates and the box size implied by your coordinate file. > > Mark > > > Otherwise the trajectory looks OK (methane moving around inside the >> cylinder). If I go on to use the conf.gro file for an mdrun, it runs to >> completion and generates what looks like a reasonable trajectory, however >> the output again contains NaN i.e: >> >> Energies (kJ/mol) >> LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy >> nan 0.00000e+00 nan 3.36749e+01 nan >> Conserved En. Temperature Pressure (bar) >> nan 3.00010e+02 nan >> >> and calculating the Diffusion coefficient gives: >> D[ CH4] 613.6682 (+/- 97.0563) 1e-5 cm^2/s >> >> If I do the same calculation but reduce the cut-offs to 0.9. I get >> >> Energies (kJ/mol) >> LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy >> nan 0.00000e+00 nan 3.36750e+01 nan >> Conserved En. Temperature Pressure (bar) >> nan 3.00011e+02 nan >> >> D[ CH4] 237.8712 (+/- 53.5975) 1e-5 cm^2/s >> >> And for a cut-off of 1.3nm I get >> >> Energies (kJ/mol) >> LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energ >> y >> nan 0.00000e+00 nan 3.36737e+01 na >> n >> Conserved En. Temperature Pressure (bar) >> nan 2.99999e+02 nan >> >> >> D[ CH4] 19.7953 (+/- 154.0168) 1e-5 cm^2/s >> >> >> For this system, the cut-off shouldn?t need to be larger than 0.8 (I have >> plotted graphs of calculated V vs r) so it is worrying that the diffusion >> coefficient is showing such dependence on the cut-offs when they should all >> give the same result. >> >> Can anyone offer any insight into this? I?ve tried changing the timestep >> making it both larger and smaller and many other things. I?ve pasted the >> relevant parts of my files below: >> >> I?m using gromacs 4.0.5 ?at the moment running in serial. >> >> Thanks for any advice, >> >> Top file >> >> [ defaults ] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> 1 2 yes 1.0 1.0 >> ; >> ; >> [ atomtypes ] >> ; type mass charge ptype c6 c12 >> OSM 15.9994 0.00 A 0.2708 1.538176 >> >> ; >> ; Include forcefield parameters >> #include "CH4.itp" >> ; >> ; >> [ moleculetype ] >> ; Name nrexcl >> MCM 3 >> [ atoms ] >> ; nr type resnr residue atom cgnr charge >> mass >> 1 OSM 1 MCM OSM 1 0 15.9994 >> 2 OSM 1 MCM OSM 2 0 15.9994 >> ..etc >> 2127 OSM 1 MCM OSM 2127 0 15.9994 >> 2128 OSM 1 MCM OSM 2128 0 15.9994 >> >> >> [ system ] >> ; Name >> CH4 in MCM >> >> [ molecules ] >> ; Compound #mols >> MCM 1 >> CH4 10 >> >> CH4.itp file >> >> [ atomtypes ] >> ; type mass charge ptype c6 c12 >> CH4 16.043 0.00 A 0.3732 1.24650457 >> ; >> [ moleculetype ] >> ; name nrexcl >> CH4 2 >> >> [ atoms ] >> ; nr type resnr residu atom cgnr charge mass >> 1 CH4 1 CH4 CH4 1 0.00 16.043 >> >> >> >> .mdp file >> >> ; >> ; File 'mdout.mdp' was generated >> ; By user: jwillia4 (353773) >> ; On host: vlxhead2 >> ; At date: Fri Jun 26 15:47:37 2009 >> ; >> ; VARIOUS PREPROCESSING OPTIONS >> ; Preprocessor information: use cpp syntax. >> ; e.g.: -I/home/joe/doe -I/home/mary/hoe >> include = -I../top >> ; e.g.: -DI_Want_Cookies -DMe_Too >> define = >> >> ; RUN CONTROL PARAMETERS >> integrator = steep >> ; Start time and timestep in ps >> tinit = 0 >> dt = 0.0001 >> > dt = 0.1 fs are you sure??
> nsteps = 100000 >> ; For exact run continuation or redoing part of a run >> ; Part index is updated automatically on checkpointing (keeps files >> separate) >> simulation_part = 1 >> init_step = 0 >> ; mode for center of mass motion removal >> comm-mode = linear >> ; number of steps for center of mass motion removal >> nstcomm = 1 >> ; group(s) for center of mass motion removal >> comm-grps = >> >> ; LANGEVIN DYNAMICS OPTIONS >> ; Friction coefficient (amu/ps) and random seed >> bd-fric = 0 >> ld-seed = 1993 >> >> ; ENERGY MINIMIZATION OPTIONS >> ; Force tolerance and initial step-size >> emtol = >> emstep = 0.001 >> ; Max number of iterations in relax_shells >> niter = >> ; Step size (ps^2) for minimization of flexible constraints >> fcstep = >> ; Frequency of steepest descents steps when doing CG >> nstcgsteep = >> nbfgscorr = >> >> >> ; OUTPUT CONTROL OPTIONS >> ; Output frequency for coords (x), velocities (v) and forces (f) >> nstxout = 100 >> nstvout = 100 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file >> nstlog = 100 >> nstenergy = 100 >> ; Output frequency and precision for xtc file >> nstxtcout = 100 >> 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 >> ; nblist update frequency >> nstlist = >> ; ns algorithm (simple or grid) >> ns_type = grid >> ; Periodic boundary conditions: xyz, no, xy >> pbc = xyz >> periodic_molecules = yes >> ; nblist cut-off >> rlist = 1.7 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> ; Method for doing electrostatics >> coulombtype = Cut-off >> rcoulomb-switch = 0 >> rcoulomb = 1.7 >> ; Relative dielectric constant for the medium and the reaction field >> epsilon_r = >> epsilon_rf = >> >> ; Method for doing Van der Waals >> vdw-type = Cut-off >> ; cut-off lengths >> rvdw-switch = 0 >> rvdw = 1.7 >> ; Apply long range dispersion corrections for Energy and Pressure >> DispCorr = No >> ; Extension of the potential lookup tables beyond the cut-off >> table-extension = >> ; Seperate tables between energy group pairs >> energygrp_table = >> >> >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters >> pme_order = >> ewald_rtol = 1e-05 >> ewald_geometry = 3d >> epsilon_surface = 0 >> optimize_fft = yes >> >> ; IMPLICIT SOLVENT ALGORITHM >> implicit_solvent = No >> >> >> ; OPTIONS FOR WEAK COUPLING ALGORITHMS >> ; Temperature coupling >> tcoupl = no >> ; Groups to couple separately >> tc-grps = >> ; Time constant (ps) and reference temperature (K) >> tau_t = >> ref_t = >> >> ; Pressure coupling >> Pcoupl = No >> Pcoupltype = >> ; Time constant (ps), compressibility (1/bar) and reference P (bar) >> tau-p = >> compressibility = >> ref-p = >> ; Scaling of reference coordinates, No, All or COM >> refcoord_scaling = no >> ; Random seed for Andersen thermostat >> andersen_seed = >> >> >> ; GENERATE VELOCITIES FOR STARTUP RUN >> gen_vel = no >> gen_temp = 300 >> gen_seed = 173529 >> >> ; OPTIONS FOR BONDS >> constraints = none >> ; Type of constraint algorithm >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration >> continuation = no >> ; Use successive overrelaxation to reduce the number of shake iterations >> Shake-SOR = no >> ; Relative tolerance of shake >> shake-tol = 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix >> lincs-order = 4 >> ; Number of iterations in the final step of LINCS. 1 is fine for >> ; normal simulations, but use 2 to conserve energy in NVE runs. >> ; For energy minimization with constraints it should be 4 to 8. >> lincs-iter = 1 >> ; Lincs will write a warning to the stderr if in one step a bond >> ; rotates over more degrees than >> lincs-warnangle = 30 >> ; Convert harmonic bonds to morse potentials >> morse = no >> >> ; ENERGY GROUP EXCLUSIONS >> ; Pairs of energy groups for which all non-bonded interactions are >> excluded >> energygrp_excl = >> >> >> ; Non-equilibrium MD stuff >> acc-grps = >> accelerate = >> freezegrps = MCM >> freezedim = Y Y Y >> cos-acceleration = 0 >> deform = >> >> >> >> >> >> >> _______________________________________________ > 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 > Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA
_______________________________________________ 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