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
--
========================================
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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