<br><br>----- Original Message -----<br>From: teklebrh@ualberta.ca<br>Date: Monday, June 28, 2010 6:01<br>Subject: [gmx-users] Error in MD simulation<br>To: jalemkul@vt.edu, Discussion list for GROMACS users <gmx-users@gromacs.org><br><br>> Dear Gromacs users,<br>> <br>> First I have to mention few points. I read all the LINCS error <br>> and tried a number of options.<br>> <br>> 1, Minimized well the system. and the Epot and Max Forces are <br>> very resonable.<br>> <br>> Steepest Descents converged to Fmax < 100 in 379 steps<br>> Potential Energy = -1.0573750e+05<br>> Maximum force = 8.0876366e+01 on <br>> atom 1117<br>> Norm of force = 8.7360611e+00<br>> <br>> 2, Equlibrate well the system. It works for 100ps<br>> <br>> Once I run NPT simulation using the following .mdp parameter set <br>> it shows the following error.<br>> <br>> ; The etire lines starting with ';' ARE COMMENTS<br>> <br>> title = NPT <br>> equilibration using the berendsen thermostat and barostat <br>> Title of run<br>> cpp = /usr/bin/cpp ; location of cpp on linux<br>> <br>> ; The following lines tell the program the standard locations <br>> where to find certain files<br>> <br>> ; VARIOUS PREPROCESSING OPTIONS<br>> ; Preprocessor information: use cpp syntax.<br>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe<br>> include =<br>> <br>> ; e.g.: -DI_Want_Cookies -DMe_Too<br>> <br>> ; RUN CONTROL PARAMETERS<br>> <br>> integrator = md ; leap-frog integrator<br>> ; Start time and timestep in ns<br>> tinit = 0<br>> dt = 0.002 ; 2fs<br>> nsteps = 500000 ; 2*500 = 1ns<br>> <br>> ; THOSE OPTIONS REMOVE MOTION OF THE ASPHALTENE MODEL COMPUNDS <br>> RELATIVE TO THE SOLVENT/IONS<br>> <br>> ; mode for center of mass motion removal<br>> comm-<br>> mode = Linear<br>> ; number of steps for center of mass motion removal<br>> nstcomm = 1<br>> ; group(s) for center of mass motion removal<br>> comm-<br>> grps = System<br>> <br>> ; LANGEVIN DYNAMICS OPTIONS<br>> ; Friction coefficient (amu/ps) and random seed<br>> bd-<br>> fric = 0<br>> ld-<br>> seed = 1993<br>> <br>> ; ENERGY MINIMIZATION OPTIONS<br>> ; Force tolerance and initial step-size<br>> emtol = 200<br>> emstep = 0.01<br>> <br>> ; Frequency of steepest descents steps when doing CG<br>> nstcgsteep = 1000<br>> nbfgscorr = 10<br>> <br>> ; OUTPUT CONTROL OPTIONS<br>> <br>> ; Output frequency for coords (x), velocities (v) and forces (f)<br>> nstxout = 2000<br>> nstvout = 2000<br>> nstfout = 0<br>> ; Output frequency for energies to log file and energy file<br>> nstlog = 1000<br>> nstenergy = 1000<br>> ; Output frequency and precision for xtc file<br>> nstxtcout = 1000<br>> xtc-<br>> precision = 1000<br>> <br>> <br>> ; This selects the subset of atoms for the xtc file. You can<br>> ; select multiple groups. By default all atoms will be written.<br>> xtc-<br>> grps = BIS HEP<br>> ; Selection of energy groups<br>> energygrps = BIS HEP<br>> <br>> ; NEIGHBORSEARCHING PARAMETERS<br>> <br>> ; nblist update frequency<br>> nstlist = 5<br>> ; ns algorithm (simple or grid)<br>> ns-<br>> type = grid<br>> ; Periodic boundary conditions: xyz, no, xy<br>> pbc = xyz<br>> ; nblist cut-off<br>> rlist = 1.2<br>> <br>> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>> <br>> ; Method for doing electrostatics<br>> coulombtype = PME<br>> rcoulomb = 1.2<br>> <br>> <br>> ; Method for doing Van der Waals<br>> vdw-<br>> type = Cut-off<br>> ; cut-off lengths<br>> rvdw = 1.2<br>> <br>> ; Apply long range dispersion corrections for Energy and Pressure<br>> DispCorr = EnerPres ; account for the cut-off vdw scheme<br>> <br>> ; Spacing for the PME/PPPM FFT grid<br>> fourierspacing = 0.16<br>> <br>> ; EWALD/PME/PPPM parameters<br>> pme_order = 4<br>> ewald_rtol = 1e-05<br>> ewald_geometry = 3d<br>> <br>> ; IMPLICIT SOLVENT ALGORITHM<br>> implicit_solvent <br>> = No<br>> <br>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>> ; Temperature coupling is on<br>> tcoupl = V-rescale; modified berendsen thermostat<br>> ; Groups to couple separately<br>> tc-<br>> grps = BIS HEP ; three coupling gropus<br>> ; Time constant (ps) and reference temperature (K)<br>> tau-<br>> t = 0.1 0.1 ; time constant<br>> ref-<br>> t = 298 298 ; reference temprature<br>> ; Pressure coupling is on<br>> Pcoupl = berendsen; Pressure coupling is on<br>> Pcoupltype = Isotropic<br>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>> tau-<br>> p = 3 3<br>> compressibility = 1.47e-4 1.47e-4 ; isothermal compressibility, bar^-1<br>> ref-<br>> p = 1 1<br>> ; Random seed for Andersen thermostat<br>> andersen_seed = 815131<br>> <br>> ; GENERATE VELOCITIES FOR STARTUP RUN<br>> gen-<br>> vel = yes ; assign velocities from Maxwell distribution (MXD)<br>> gen-<br>> temp = 298 ; temperature for MXD<br>> gen-<br>> seed = 173529 ; used to initialize random generator for random velocities<br>> <br>> ; OPTIONS FOR BONDS<br>> constraints = all-bonds<br>> ; Type of constraint algorithm<br>> constraint-algorithm = Lincs<br>> ; Do not constrain the start configuration<br>> ; Highest order in the expansion of the constraint coupling matrix<br>> lincs-<br>> order = 4<br>> ; Number of iterations in the final step of LINCS. 1 is fine for<br>> ; normal simulations, but use 2 to conserve energy in NVE runs.<br>> ; For energy minimization with constraints it should be 4 to 8.<br>> lincs-<br>> iter = 2<br>> ; Lincs will write a warning to the stderr if in one step a bond<br>> ; rotates over more degrees than<br>> lincs-<br>> warnangle = 30<br>> ; Convert harmonic bonds to morse potentials<br>> morse = no<br>> <br>> ==========<br>> <br>> It run the simulation for quite sometime but it gives me an <br>> error of LINCS some how in the middle.<br>> <br>> I try changing some parameter sets like step size,tau-p , tau-t, <br>> lincs-warnangle but did not overcame the problem.<br><br>You are trying to equilibrate straight into NPT, which can be problematic if (for example) the density isn't right. Consider the advice in point 8 of http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation<br><br>Mark<br><br>> Step 197685, LINCS WARNING<br>> >relative constraint deviation after LINCS:<br>> >rms 0.000000, max 0.000001 (between atoms 1856 and 15982)<br>> >bonds that rotated more than 30 degrees:<br>> > atom 1 atom 2 angle previous, current, constraint length<br>> > 97 98 <br>> 35.3 0.1000 <br>> 0.1000 0.1000<br>> <br>> can some one give me an advice or help?<br>> <br>> For my other 10 MD set up it works fine but with diffrent solvents.<br>> <br>> rob<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search <br>> before posting!<br>> Please don't post (un)subscribe requests to the list. Use thewww <br>> interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php