[gmx-users] I can't figure out what is wrong with my .gro
jalemkul at vt.edu
Thu Jan 10 01:12:51 CET 2013
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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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