[gmx-users] PME grid spacing

Moeed lecielll at googlemail.com
Tue May 11 16:59:15 CEST 2010


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)

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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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