meisam valizadeh kiamahalleh wrote:
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;
The -maxwarn option should almost never be used. If you're overriding warnings
that grompp is producing, they typically only occur if the system will become
unstable. Beware.
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?
You have different bonded parameters assigned for a single bond type. You
should investigate why you've produced different parameters for the same
interaction and correct it, if necessary. If you are trying to override
existing parameters, this may be what you want. Otherwise, eliminate the
duplicate entry such that the parameters you actually wish to use are being
assigned.
2) Regarding Note 1, Is it necessary to do ionization to make the system
neutralize before minimization?
Not in this case. You have a non-integer charge of sufficiently disturbing
magnitude (i.e., it does not arise simply due to floating point arithmetic),
indicating that the charges assigned in the topology are junk.
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.
For minimization, this often happens. It is unimportant in this case.
-Justin
Thank you very much
Best regards
M.V.K
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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