[gmx-users] Problem with grompp?
Hoof, B. van
B.v.Hoof at tue.nl
Thu Apr 16 12:37:47 CEST 2009
Yes, indeed. The file topol.tpr was not re-created when I used grompp. In fact, an error was thrown by grompp stating file input/output error: minimized.gro
I am embarrased to say that I had used the command
> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -o membr.tpr -maxwarn 10
instead of
> grompp -f martini_md1.mdp -c minimised.gro -p martini.top -o membr.tpr -maxwarn 10
Unfortunately, because mdout.mdp was created correctly, I hadn't noticed this error.
Thank you everyone for your help!
Bram van Hoof
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: donderdag 16 april 2009 12:11
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Problem with grompp?
Hi Bram,
Check the creation times for topol.tpr and minimized.gro. First test
the assumption that the former was created later than the latter. If
it's not, then check the grompp output for errors. Maybe pasting it
here can help.
Cheers,
Tsjerk
On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van <B.v.Hoof at tue.nl> wrote:
> 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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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