[gmx-users] Problem with grompp?
Hoof, B. van
B.v.Hoof at tue.nl
Thu Apr 16 10:57:19 CEST 2009
Thanks for your answer. I am afraid, however, that the problem is then somewhat different. Using
grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10
should have created a new topol.tpr, should it not? It did so in previous times at least.
If someone knows where I am going wrong, please let me know.
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: woensdag 15 april 2009 18:12
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Problem with grompp?
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.
> Bram van Hoof
> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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