[gmx-users] I can't figure out what is wrong with my .gro

Justin Lemkul 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
> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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