[gmx-users] Odd protein behavior in MD

Mark Abraham mark.j.abraham at gmail.com
Thu May 22 22:00:18 CEST 2014


The usual workflow to fix these kinds of pbc issues can be found here:


On Thu, May 22, 2014 at 9:48 PM, Steve Seibold <stevesei at ymail.com> wrote:

> 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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