[gmx-users] g_traj + g_analyze and core dumped error

[gozde ergin]

Ok thanks Justin.
Than how can I get the time series of total force of the box?
g_traj gives the -af  all_force.xvg but this is for each atom not a time
series means y coordinate is the total force and x coordinate is the atom.

On Wed, Sep 16, 2015 at 5:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/16/15 11:48 AM, gozde ergin wrote:
>
>> Also I did the same calculation for only one atom and did not get any
>> error.
>>
>>
>>
> Probably because your original command will have 3*9566 floating-point
> entries per line, which likely can't even be read by GROMACS tools.  So
> analyzing one atom is fine, analyzing all of them at the same time likely
> isn't possible.
>
> -Justin
>
> On Wed, Sep 16, 2015 at 4:39 PM, gozde ergin <gozdeeergin at gmail.com>
>> wrote:
>>
>> Dear gromacs users;
>>>
>>> I am trying to estimate the force-force auto correlation function.
>>> To do that first I run the command of :
>>>
>>>   'g_traj -f tra.trr -s topol.tpr -of force.xvg'
>>>
>>> My force.xvg file covers for all atoms in simulation box which I have
>>> 9566
>>> atoms.
>>> Than I run the command of :
>>>
>>> 'g_analyze -f force.xvg -ac autocorr.xvg'
>>>
>>> however I get the error of core dumped. Here is some snapshot from
>>> screen.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *File force.xvg does not end with a newline, ignoring the last lineFile
>>> force.xvg does not end with a newline, ignoring the last lineFile
>>> force.xvg
>>> does not end with a newline, ignoring the last lineFile force.xvg does
>>> not
>>> end with a newline, ignoring the last lineInvalid line in
>>> force.xvg:....................Using zeros for the last 7819 sets.*
>>>
>>>
>>> What could be the reason of this error?
>>> I have enough free space and I am using gromacs 4.6.6
>>>
>>> bests
>>>
>>>
> --
> ==================================================
>
> 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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