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

[Xu Dong Huang]

@ Justin,

Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character? 

Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 9, 2013, at 7:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> 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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