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

[Justin Lemkul]

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
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Baltimore, MD 21201

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

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