[gmx-users] Fattal error in gmx dos

[Alexander Alexander]

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.


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?

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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