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

Xu Dong Huang xudongh at eden.rutgers.edu
Thu Jan 10 01:07:04 CET 2013

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


Thanks for any input.

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

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