From: Jana, Suvamay (sja236_at_g.uky.edu)
Date: Mon Nov 25 2013 - 20:07:31 CST
I have initially built my protein-ligand system in charmm and converted my
charmm psf file to xplor format to run simulation in namd (nvt ensemble).
In my initial charmm setup I fixed the position of some of the atoms.
I know from --
after the mass entry the next column holds an unused number (0) in namd psf
but in my psf file those are 1 instead of 0 and that is due to the fixed
position constraints used for those atoms
Is this '1 instead of 0 value in my case' - in that particular column has
any effect during namd simulations or these values are just ignored during
namd simulation (no constraint atoms move freely)?
Thanks in advance.
Graduate Student, University of Kentucky
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