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