[gmx-users] velocity was not present from trjconv

[Justin Lemkul]

On 2/12/13 9:17 AM, Albert wrote:
> Hello:
>
>   I am using Gromacs4.6 and I extract one of my frame into .gro file by command:
>
> trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro
>
> I found that the velocity information was not present in this 25ns-md.gro file:
>

Velocities are not stored in .xtc files.  They are stored in .trr files, if 
nstvout != 0 in the .mdp file.

-Justin

>
>
> Generated by trjconv : Protein t= 25000.00000
> 54178
>      1TYR      N    1   1.696   3.993   8.140
>      1TYR     H1    2   1.658   4.068   8.196
>      1TYR     H2    3   1.719   4.031   8.050
>      1TYR     H3    4   1.630   3.919   8.122
>      1TYR     CA    5   1.822   3.938   8.210
>      1TYR     HA    6   1.865   4.020   8.268
>      1TYR     CB    7   1.790   3.814   8.300
>      1TYR    HB1    8   1.883   3.770   8.336
>      1TYR    HB2    9   1.764   3.732   8.233
>      1TYR     CG   10   1.696   3.845   8.416
>      1TYR    CD1   11   1.745   3.930   8.520
>      1TYR    HD1   12   1.847   3.967   8.520
> ...
>
> Does anybody knows what happen? The final md output md.gro file do contains
> velocity information:
>
> Protein
> 54178
>      1TYR      N    1   1.747   4.039   8.153 -0.1860  0.0829  0.0094
>      1TYR     H1    2   1.694   4.084   8.226  2.0932 -0.4724  2.1614
>      1TYR     H2    3   1.804   4.115   8.117 -1.6223  0.9380 -0.5483
>      1TYR     H3    4   1.682   4.001   8.086  0.6678 -0.6031 -0.4474
>      1TYR     CA    5   1.826   3.927   8.204 -0.5364 -0.8546 -0.6273
>      1TYR     HA    6   1.892   3.958   8.285  0.3239 -2.3918 -0.7049
>      1TYR     CB    7   1.732   3.813   8.243  0.4625 -0.6033 -0.2530
>      1TYR    HB1    8   1.791   3.725   8.265 -1.7147 -1.9740  0.4749
>      1TYR    HB2    9   1.660   3.783   8.166 -0.2485  2.0549 -0.7384
>      1TYR     CG   10   1.663   3.842   8.377 -0.0029  0.0693 -0.2885
>      1TYR    CD1   11   1.739   3.893   8.481 -0.5325 -0.8010 -0.1664
>      1TYR    HD1   12   1.841   3.925   8.465  0.0708 -2.2306  0.7255
>      1TYR    CE1   13   1.680   3.925   8.606  0.5957  0.0504 -0.4752
>      1TYR    HE1   14   1.728   3.974   8.689  1.1798 -3.6443  1.5406
>
>
> THX
>
> Albert

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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