[gmx-users] g_current

[Justin Lemkul]

On 4/15/14, 4:16 PM, Nilesh Dhumal wrote:
> Justin,
>
> Thanks for information. I run g_current for other system, ionic liquids. I
> checked the velocities using gmxcheck.
>
> I run, g_current -f 500.trr -s 500.tpr -mc
> There are two columns, I am not getting which rotational and
> translational. End of the file the function is infinity. Here I pasted the
> initial part of mc.xvg
>

Based solely on the description provided in the second paragraph of g_current 
-h, I wouldn't expect to necessarily find separate ACF for rotational and 
translational components.  The same paragraph also indicates why the infinite 
value shows up at the end; you probably can't consider all time points.  Having 
never used g_current, this is all I have to go on.

Check the other output files.  The -mc option appears to be just for ACF.

-Justin

> # This file was created Tue Apr 15 15:52:34 2014
> # by the following command:
> # g_current -f 500.trr -s 500.tpr -mc
> #
> # g_current is part of G R O M A C S:
> #
> # Gravel Rubs Often Many Awfully Cauterized Sores
> #
> @    title "M\sD\N - current  autocorrelation function"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "< M\sD\N (0)\c7\CJ(t) >  (e nm/ps)\S2"
> @TYPE xy
> # time   M_D(0) J(t) acf         Integral acf
> 0.000    -0.140658               0
> 0.001    -0.147092      -0.000386539
> 0.002    -0.151369      -0.00119497
>
> 49.993    -2.19596         51.7085
> 49.994    -2.23022         51.6964
> 49.995    -2.25746         51.6842
> 49.996    -2.27946         51.6718
> 49.997    -2.29797         51.6592
> 49.998     -2.3135         51.6466
> 49.999    -2.32483         51.6339
> 50.000        -inf         51.6211
>
> Nilesh
>
>
>
>>
>> On 4/15/14, 2:27 PM, Nilesh Dhumal wrote:
>>> Here is full gmxcheck
>>>
>>> Checking file water.trr
>>> trn version: GMX_trn_file (single precision)
>>> Reading frame       0 time    0.000
>>> # Atoms  2592
>>> Last frame        100 time   20.000
>>>
>>>
>>> Item        #frames Timestep (ps)
>>> Step           101    0.2
>>> Time           101    0.2
>>> Lambda         101    0.2
>>> Coords         101    0.2
>>> Velocities       0
>>
>> There you have it; you didn't save 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 601
>> 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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