[gmx-users] Odd protein behavior in MD

Steve Seibold stevesei at ymail.com
Thu May 22 21:49:20 CEST 2014

I ran a 8 ns simulation on a small protein in a water box using PBC. I then calculated the RMS using g_rms command. When I plotted the outcome my rms graph looked like a Histogram instead of a rms plot. I then took a region of the trajectories and view them in VMD. The protein starts out ok, but suddenly blows up in the since that separate parts of the protein went to the four corners of the box...I thought maybe this was a problem of PBC where parts of my protein were leaving the box and so, I attempted to center protein and water back into the center of the box using the following procedure:

trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc

However, this did not correct the problem...Can someone please inform as to what the problem is??? The total energy and potential energy looks ok and so, I am lost as to what is happening or how to fix it.

Thanks, Steve

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