On 1/9/13 7:07 PM, Xu Dong Huang wrote:
Dear all,
I created this .gro file following the gromacs format. But when I load it into
VMD, it doesn't show the structure or molecule, and I have made many .gro
before this one, and learned from many mistakes, but for this one, I don't know
what I did wrong. I still proceeded to do simulation anyway and when I do
energy minimization, I get an error of infinite normal force and etc (which I
read past gmx list question that an atom is severely overlapping and causing
the complication). Since I can't even view the .gro structure i made in VMD,
I'm going to go ahead and assume there is something wrong with my initial
structure to begin with, but I don't know where.
Here is the link to my .gro file + topology
https://docs.google.com/open?id=0BwQvutOxRUqkNFMtSmVDanlwRFE
https://docs.google.com/open?id=0BwQvutOxRUqkRkNQR2RYS0d6aDA
https://docs.google.com/open?id=0BwQvutOxRUqkaXV4ZmJaTks5Zzg
The last line of the .gro file (box vectors) does not end in a newline
character. I discovered this by running:
wc -l star.gro
which returned 103, which would indicate that there should be 100 atoms in
addition to a title line, number of atoms, and box vectors. Since there are 101
listed atoms, I knew there was a problem, likely with the last line. Adding a
newline character allows the structure to be opened in VMD.
-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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