REMD trajectory files

GROMACS version:2020
GROMACS modification: Yes/
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I am reading Mark Abraham’s tutorial on REMD. Can I ask

  1. “sim[0123]” is used to run REMD among 4 temperatures in the sim0, sim1, sim2, sim3 subdirectories. How to name the folders to have more than 10 subdirectories?

  2. There seems to be no xtc/trr files generated after REMD. So how to analyse the trajectories?

  3. In the “De-multiplexing an REMD trajectory in GROMACS” Section, it is mentioned that “GROMACS exchanges coordinates (instead of temperature)” but there is a way to obtain “continuous coordinates” (, trjcat -demux). My understanding is
    ) each subdirectory represents a particular temperature with discontinuous coordinates in the trajectory file
    ) if “continuous coordinates” is obtained, it is a trajectory with coordinate frames from different temperatures.
    Is that correct?

  4. Is there a force-field to recommend for a protein of 400 residues? I do not have any other non-canonical amino acids. My interest temperature is around 340K. The REMD temperature generator uses the OPLS/AA forcefield, can I use it?

Can someone take a look at my question? Here is the files in the provided folder, in which xtc or trr files do not exist.


I was told, “nstxout = 0” makes the output trajectory not written.

nstxout, nstvout, and nstfout set the output frequency for .trr files. If they are all set to zero, hen no .trr file is written. nstxout-compressed controls the output frequency for .xtc files. If you want .xtc output, this parameter must be non-zero.

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