[gmx-users] Catenation and sampling

suniba shuaib suniba88chemistry at gmail.com
Thu Mar 2 17:40:36 CET 2017

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

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

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