On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1star O4 1 0.000 0.000 0.000
1star O1 2 0.430 0.000 0.000
1star O1 3 0.860 0.000 0.000
1star O1 4 1.290 0.000 0.000
1star O1 5 1.720 0.000 0.000
1star O1 6 2.150 0.000 0.000
1star O1 7 2.580 0.000 0.000
1star O1 8 3.010 0.000 0.000
1star O1 9 3.440 0.000 0.000
1star O1 10 3.870 0.000 0.000
1star O1 11 4.300 0.000 0.000
1star O1 12 4.730 0.000 0.000
1star O1 13 5.160 0.000 0.000
1star O1 14 5.590 0.000 0.000
1star O1 15 6.020 0.000 0.000
1star O1 16 6.450 0.000 0.000
1star O1 17 6.880 0.000 0.000
1star O1 18 7.310 0.000 0.000
1star O1 19 7.740 0.000 0.000
1star O1 20 8.170 0.000 0.000
...
and for the output .gro after editconf, here is what it shows (I don't know why
the formats are kind of shifted, )
star polymer
201
1star O4 1 11.921 11.921 16.195
1star O1 2 12.351 11.921 16.195
1star O1 3 12.781 11.921 16.195
1star O1 4 13.211 11.921 16.195
1star O1 5 13.641 11.921 16.195
1star O1 6 14.071 11.921 16.195
1star O1 7 14.501 11.921 16.195
1star O1 8 14.931 11.921 16.195
1star O1 9 15.361 11.921 16.195
1star O1 10 15.791 11.921 16.195
1star O1 11 16.221 11.921 16.195
1star O1 12 16.651 11.921 16.195
1star O1 13 17.081 11.921 16.195
1star O1 14 17.511 11.921 16.195
1star O1 15 17.941 11.921 16.195
...
The issue here is spacing. The files have tabs in them, which break the
mandatory alignment for a .gro file. The atoms did not display because VMD
could not correctly read the coordinate fields.
-Justin
--
========================================
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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