GROMACS modification: Yes/
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I am reading Mark Abraham’s tutorial on REMD. Can I ask
“sim” 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?
There seems to be no xtc/trr files generated after REMD. So how to analyse the trajectories?
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?
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?