Output only protein .dcd

From: Nur Aida Abdul Rahim (aida_at_MIT.EDU)
Date: Tue Sep 14 2004 - 13:41:38 CDT

Hello all,

Does anyone know if it is possible to output a .dcd file with only the values
for the protein in my system? If so, how could I go about doing this? This is
because I am only interested at looking at the trajectory of my protein
throughout SMD and not the water molecules. My system is ~150,000 atoms large
and consists of a protein in a waterbox. Running an SMD simulation of 1ns long
and saving at every 0.5ps produces a .dcd file that is 2GB large. If I could
output only for the protein, the size of the file would be smaller and I could
maybe load it onto a .psf of just the protein without surrounding water...?
Maybe. Any advice would be greatly appreciated, thanks!


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