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!
Greetings,
Bram van Hoof
mdout.mdp
Description: mdout.mdp
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