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I have started trying out Zephyr for simulating and I have run into a problem. I simulated a molecule for 30,000ps, this finished successfully, and I could view the resulting simulation in VMD no problem. Now, when I load up VMD again, load in the original (and even the processed .pdb file), I cannot then load the .trr file into the molecule. One thing I have noticed is that the number of atoms don't match, my original model has 1581 atoms, but the trajectory has 1583. Can anyone help please.

I have found that I can load the .gro file, and then load the .trr data into that. However, I was sure that I had been able to load the data into the original .pdb file at some point.