[gmx-users] Problem with grompp?

Hoof, B. van B.v.Hoof at tue.nl
Wed Apr 15 17:25:15 CEST 2009

Hi everyone,

Since I am a new user of Gromacs, this problem is probably rather trivial, but I hope one of you would like to help me nonetheless. I have created a starting structure in a not very optimal situation, which I have then minimized. To continue, I would like to equilibrate the system further using leap-frog MD. To do so, I have used grompp in the following way:
grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10

This creates the following mdout.mdp: see attachment

Now as far as I can see, using the command `mdrun -v -c md_run.gro' should result in performing a 1,000,000 iteration md simulation of this system. However, when I issue that command, instead what I get is this:
                         :-)  G  R  O  M  A  C  S  (-:

                 Good ROcking Metal Altar for Chronical Sinners

                            :-)  VERSION 4.0.4  (-:


                                :-)  mdrun  (-:

Option     Filename  Type         Description

Getting Loaded...
Reading file topol.tpr, VERSION 4.0.4 (single precision)
Loaded with Money

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =        10000
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.23314e+20 Fmax= 2.04950e+19, atom= 11163
Step=    2, Dmax= 1.2e-02 nm, Epot=  5.22616e+17 Fmax= 2.22256e+20, atom= 10863
Step=    3, Dmax= 1.4e-02 nm, Epot=  1.46382e+17 Fmax= 7.52962e+17, atom= 10593
Step=    4, Dmax= 1.7e-02 nm, Epot=  1.21703e+17 Fmax= 3.72098e+16, atom= 10331
Step=    5, Dmax= 2.1e-02 nm, Epot=  2.22862e+16 Fmax= 4.87326e+18, atom= 10857
Step=    6, Dmax= 2.5e-02 nm, Epot=  1.09032e+16 Fmax= 4.39937e+15, atom= 15106
Step=    7, Dmax= 3.0e-02 nm, Epot=  1.81517e+15 Fmax= 6.07049e+14, atom= 15230
Step=    8, Dmax= 3.6e-02 nm, Epot=  2.84750e+14 Fmax= 9.82848e+14, atom= 14675
Step=    9, Dmax= 4.3e-02 nm, Epot=  2.33131e+14 Fmax= 2.39469e+13, atom= 11419
Step=   10, Dmax= 5.2e-02 nm, Epot=  7.23189e+12 Fmax= 2.72305e+14, atom= 14565
Step=   11, Dmax= 6.2e-02 nm, Epot=  3.19510e+12 Fmax= 4.82192e+12, atom= 10638
Step=   13, Dmax= 3.7e-02 nm, Epot=  1.82616e+12 Fmax= 1.11184e+13, atom= 11929
[... etc.....]

This is a minimization using the steepest descent algorithm. What am I doing wrong here?

Thank you in advance for your kind help!

Bram van Hoof

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