[gmx-users] Catenation and sampling

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 3 08:09:58 CET 2017


You can't concatenate trajectories and expect them to behave as if they
were continuous. Apparently three of your simulations show similar
behaviour and two different, perhaps explained by a transition in your
equilibration run after 2 ns.

In the limit of ergodic sampling, your protocol for five runs would be
fine, but by starting them all from similar systems, you build in a
starting similarity that you now have to correct for. That period of
similarity is hard to measure, but will be lower if you generate different
velocities before five separate equilibrations.


On Thu, 2 Mar 2017 17:40 suniba shuaib <suniba88chemistry at gmail.com> wrote:

> Dear users and experts
> I have simulated a protein in water using OPLS-AA force field. Initially I
> performed a 5 ns simulation and then extracted frames out of it e.g. at
> 1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each
> extracted frame. Now I have five 100 ns trajectories (A.xtc, B.xtc, C.xtc
> etc..). My question is how should I catenate these trajectories in order to
> ensure good sampling. When I used gmx trjcat with -settime flag, I obtained
> RMSD and Rg which showed very high fluctuation till 150 ns and then was
> quiet stable till the end of 500ns. I am confused if these extra high
> fluctuations are due to poor sampling or improper catenation. Please help
> me.
> The fluctuations in RMSD were between 0.2-1.8 nm till 150 ns and then RMSD
> stayed between 1.0-1.1 nm.
> With Regards
> Suniba
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