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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