Dear All I am working on protein unfolding simulation in gromacs. when I do a production run on 32 node HPC I get .trr file along with .gro. when I try to visualize this files in VMD I see erratic large movement of atoms in the trajectory. With same .mdp files when I did smaller run of 2ns on single PC and viewed .trr and .gro in VMD, the movemnt of atom was smooth. Why this is happening. When I used the command g_filter to produce lowpass.xtc with -nf 10 I got the smooth movement of atoms. Is it always essential to use g_filter with .trr file of HPC multinode output. what is the difference between lowpass.xtc and highpass.xtc. For the pupose of RMSD calculation should I use the output of g_filter i.e. lowpass.xtc or the original .trr file. I am new in this field so excuse me for some basic mistakes . Any suggestion and help will highly appreciated. Thanking you in advance. msnayeem
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