[gmx-users] g_current

[Nilesh Dhumal]

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

# 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
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> 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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