[gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

[Mark Abraham]

Sampo Karkola wrote:
> Thanks for the quick answer!
> 
> I did gmxcheck for the em and md tpr-files and they do differ on lot of 
> things. However, I do not know what these differences mean. I was 
> looking for some documentation about the output from gmxcheck but 
> couldn't find any, so if someone has some guides on how to read the 
> output, I'd be grateful. Or if someone would be kind enough to take a 
> look at the output at http://www.helsinki.fi/~karkola/gmxcheck.tar.gz

It's a bit of a dark art, but I had a look and there is something 
changing with your force field description, which leads me back to the 
.top file.

>>> Luckily, I had an older simulation (with gromacs 3.2.1, now I'm using 
>>> 3.3.1) with the same ligand (except one atom type is changed from NR 
>>> in the old topology to N in new topology) alone and there the 
>>> energies decreased as they should. To study the differences in the 
>>> ligand-alone simulations, I performed an mdrun with the old tpr file 
>>> (mdrun -s old.tpr -o new_run -c new_run...) and the energies 
>>> decreased again, as they should. Next, I grompped a new tpr-file from 
>>> the old gro, top and mdp files, got a new tpr file and simulated it 
>>> resulting in decreasing energies again. But when I try to do the 
>>> whole process from the beginning using the same pdb file as in the 
>>> older run something goes differently and the mdrun produces rising 
>>> energies.

You should diff your old and new .top files to see what is different 
there. If nothing seems to be the culprit, please upload a sample and a 
diff and I'll look.

Mark