Yes, I also think the *.tpr after -s maybe the reference state. However, In this way, why in the manual it says like this? "With the option -od the root mean square deviation with respect to the reference structure is calculated" What about without -od, should there be no reference structure or the reference structure is taken as average over the trajectory?
Thanks! >Pan Wu wrote: >> Hi everyone, >> Thank you for answering my former questions, it really help me, the >> new gmx-er a lot~ >> Here is another question about reference state of RMSF. >> In the manual, it shows "g_rmsf computes the root mean square >> fluctuation (RMSF, i.e. standard deviation) of atomic positions >> after (optionally) fitting to a reference frame". So in this way, can I >> choose the reference frame from *.tpr file or the coordinate average >> over the whole trajectory? If Gromacs can, how? > >I believe the reference structure is taken from whatever structure file is given >to the -s flag, so in principle you could provide any frame from the trajectory, >as well as the initial one, or some average structure (from, i.e. g_cluster or >something similar). > >-Justin
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