Hoof, B. van wrote:
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!
If you use default names (i.e., topol.tpr for output), you can easily confuse
yourself and wind up running the wrong input file. The mdout.mdp file you
posted should correspond to MD; most likely you've just re-run the same .tpr
file that you used for minimization.
-Justin
Greetings,
Bram van Hoof
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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