[gmx-users] Problem with grompp?

[Hoof, B. van]

Hi Justin,

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.

Kind regards,
Bram



-----Original Message-----
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.

-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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