[gmx-users] Fattal error in gmx dos

[Justin Lemkul]

On 1/29/16 7:10 PM, Alexander Alexander wrote:
> Thank you for your response.
>
> Then please how can I have case.trr and case.tng? I had gen_vel = yes in my
> case.mdp but no velocity was stored somewhere, I just had case.cpt.
> The same error showed up when I used case.cpt instead of case.trr.
>

The gen_vel keyword has nothing to do with saving information; it randomizes 
velocities at the outset of the simulation (gen = generate, not save).

You want to look through 
http://manual.gromacs.org/documentation/5.1.1/user-guide/mdp-options.html#output-control

>
> One more question is that what the meaning of the following sentence is
> that comes in the gmx dos explanation?
>   "In order for this to be meaningful the velocities must be saved in the
> trajecotry with sufficiently high frequency such as to cover all
> vibrations"?
> How should I know that that the frequency is high enough to cover all the
> vibration? How to reach this point?
>

The next sentence reads:

"For flexible systems that would be around a few fs between saving."

-Justin

> Thanks,
>
> Regards,
> Alex
>
> On Sat, Jan 30, 2016 at 12:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/29/16 6:48 PM, Alexander Alexander wrote:
>>
>>> Dear Gromacs user,
>>>
>>> After convergence of my MD simulation where I got my case.xtc file but not
>>> case.trr directly, I produced the the case.trr file by the "gmx trjconv -f
>>> case.xtc -o case.trr" towards my "gmx dos" calculation. (I had "gen_vel =
>>> yes" in my case.mdp)
>>> Then I got below Fatal error when I invoked the gmx dos command normally
>>> as
>>> "gmx dos -f case.trr -s case.tpr -vacf case_va.xvg -mvacf case_mv.xvg -dos
>>> case_dos.xvg -g dos.log"
>>>
>>> Program gmx dos, VERSION 5.1-rc1
>>> Source code file:
>>> /home/alex/gromacs-5.1-rc1/src/gromacs/fft/fft_fftw3.cpp,
>>> line: 309
>>>
>>> Fatal error:
>>> Error initializing FFTW3 plan.
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>> I would be so appreciated if one could explain the potential reason for
>>> this error.
>>>
>>>
>> Converting .xtc to .trr does not magically produce velocities (which are
>> not saved in an .xtc), so you cannot use the resulting .trr file for
>> anything that requires velocities.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================