Dear GROMACS experts, Initially I wanted to do MD for a stack of hexane molecules. MD showed very high repulsion potential. On the recommendation of Justin, I simplified the problem and now I have only one Hexane molecule.
1- I dont know why I do not get the written pdb files normally generated after MD! I want to watch the trajectory. 2- Could you please kindly take a look at energy values and let me know if values are reasonable so that I can proceed to building stack of hexane molecules. Pon 3- Please help me understand NOTE 2 in output.grompp_md (end of this post message) Thank you for you help and time. **************************** **********************************************output.mdrun_em: Getting Loaded... Reading file Hexane_em.tpr, VERSION 4.0.7 (double precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 200 Step= 0, Dmax= 1.0e-02 nm, Epot= 1.65572e+01 Fmax= 2.05661e+02, atom= 3 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 1 steps Potential Energy = 1.65571528230744e+01 Maximum force = 2.05661442550269e+02 on atom 3 Norm of force = 1.43113884736035e+02 ********************** ****************************************************************************************output.mdrun_md: Getting Loaded... Reading file Hexane_md.tpr, VERSION 4.0.7 (double precision) Loaded with Money Back Off! I just backed up Hexane_md.tpr.trr to ./#Hexane_md.tpr.trr.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Hexane' 5000 steps, 5.0 ps. ^Mstep 0^Mstep 100, remaining runtime: 0 s ^Mstep 200, remaining runtime: 0 s ^Mstep 300, remaining runtime: 0 s ^Mstep 400, remaining $ Writing final coordinates. Back Off! I just backed up Hexane_after_md.gro to ./#Hexane_after_md.gro.1# ^Mstep 5000, remaining runtime: 0 s Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 8.000 8.000 100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 0.056 2.535 54.011 0.444 gcq#41: "It'll Cure Your Asthma Too !" (F. Zappa) ************************************************************************ Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 11 data sets All averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Angle 25.3845 5.73205 4.93305 -1.01102 -10.1122 LJ-14 4.10469 1.15875 1.15324 -0.0390717 -0.390795 Coulomb-14 -2.75709 0.405546 0.405507 0.00194442 0.0194481 LJ (SR) -2.81209 0.366057 0.365356 -0.00784402 -0.0784559 Coulomb (SR) 13.5848 0.325985 0.325828 -0.00350364 -0.0350434 Potential 41.2684 6.06845 5.15746 -1.10757 -11.0779 Kinetic En. 47.2772 5.02364 4.99139 0.196848 1.96887 Total Energy 88.5456 3.8207 2.77186 -0.910721 -9.10903 Temperature 299.269 31.8001 31.5959 1.24606 12.4631 Pressure (bar) -0.0933911 47.1966 47.1951 -0.126676 -1.26701 T-HEX 299.269 31.8001 31.5959 1.24606 12.4631 Heat Capacity Cv: 12.6866 J/mol K (factor = 0.011291) ****************************************************************************************************************************************************************** title = Hexane cpp = /lib/cpp ; Run control integrator = md dt = 0.001 ; ps ! nsteps = 5000 ; total 1.0 ps. nstcomm = 1 ; frequency for center of mass motion removal ; Output control nstenergy = 10 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 1 ; frequency to write coordinates/velocity/force to output trajectory file nstvout = 0 nstfout = 10 nstlog = 10 ; frequency to write energies to log file ; Neighbor searching nstlist = 10 ; neighborlist will be updated at least every 10 steps ;ns_type = grid ; Electrostatics/VdW coulombtype = PME vdw-type = cut-off ; Cut-offs rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Temperature coupling Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ; Pressure coupling: Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Velocity generation Generate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz **********************************************************************************************************output.grompp_md NOTE 1 [file md11.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Hexane' processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat Making dummy/rest group for Acceleration containing 20 elements Making dummy/rest group for Freeze containing 20 elements Making dummy/rest group for Energy Mon. containing 20 elements Making dummy/rest group for VCM containing 20 elements Number of degrees of freedom in T-Coupling group HEX is 38.00 Making dummy/rest group for User1 containing 20 elements Making dummy/rest group for User2 containing 20 elements Making dummy/rest group for XTC containing 20 elements Making dummy/rest group for Or. Res. Fit containing 20 elements Making dummy/rest group for QMMM containing 20 elements T-Coupling has 1 element(s): HEX Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Estimate for the relative computational load of the PME mesh part: 0.97 NOTE 2 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing writing run input file... There were 2 notes Back Off! I just backed up Hexane_md.tpr to ./#Hexane_md.tpr.1# gcq#92: "Once Again Let Me Do This" (Urban Dance Squad) :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: processing topology... turning all bonds into constraints... Analysing residue names: There are: 1 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 25x25x25, spacing 0.120 0.120 0.120 This run will generate roughly 4 Mb of data
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