[gmx-users] Warning and Notes in Grompp for minimization

meisam valizadeh kiamahalleh meisam488 at gmail.com
Sat Aug 20 22:04:20 CEST 2011

Dear gmx-users
Good day to you
I have a system including carbon nanotube (1260atoms) and 18 Cisplatin
molecules (198atoms) =1458atoms. I have created the topology file of the
system and now I would like to run minimization on this system.
The content of my mdp file is as below;

define               = -DFLEXIBLE
constraints          = none
integrator           = steep
dt                   = 0.002     ; ps !
nsteps               = 400
nstlist              = 10
ns_type              = grid
rlist                = 1
coulombtype          = PME
rcoulomb             = 1
vdwtype              = cut-off
rvdw                 = 1.4
optimize_fft         = yes
;        Energy minimizing stuff
emtol                = 1000.0
emstep               = 0.01

After entering the command; grompp -f mdmin1.mdp -c SWCNT-DDP-box.pdb -p
SWCNT-DDP2.top -o SWCNT-DDP2.tpr -maxwarn 5 , However a wrong TPR file is
generated, I also get 2 notes and 1 warning as stated below;
WARNING 1 [file ffbonded.itp, line 2705]:
  Overriding Bond parameters.

  old: 0.151 292880 0.151 292880
  new: C        C        1     0.14210   478900

Generated 347361 of the 347361 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 347361 of the 347361 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'ICE'

NOTE 1 [file SWCNT-DDP2.top, line 15383]:
  System has non-zero total charge: -3.097796e-01

Analysing residue names:
There are:     2      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 4371.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 120x120x120, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.97

NOTE 2 [file mdmin1.mdp]:
  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

This run will generate roughly 0 Mb of data.

My questions:
1) May I know whether warning 1 should be taken serious?If yes, Then how to
solve it?
2) Regarding Note 1, Is it necessary to do ionization to make the system
neutralize before minimization?
3) Regarding Note 2, Is there anything wrong with my mdp file or it is
because of using a computer with small processor. Actually I just tried to
do this minimization on my laptop for the first time. If the processor is
too small for this calculation, I may be able to work with our cluster if it
is advised.

Thank you very much
Best regards
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