REMD trajectory files

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1

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” (demux.pl, 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?

2

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.

image

3

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

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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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