From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Mon Oct 18 2010 - 09:32:07 CDT
I am trying to do a second run on a simulation of a solvated dipeptide. I have successfully run 2 simulations on both of two of the three protonated states of the peptide, but for the third protonation state during the second (restart) run I encounter the following problem:
Reason: FATAL ERROR: Couldn't open DCD file /run2_solvatedpeptide.dcd: Permission denied
Charm++ fatal error:
FATAL ERROR: Couldn't open DCD file /run2_solvatedpeptide.dcd: Permission denied
I have checked to see that the respective files generated in the first run are where they have to be.
Any help would be appreciated
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of sunita gupta [sunita.bio_at_gmail.com]
Sent: Monday, October 18, 2010 12:52 PM
Subject: namd-l: High RMSD of Coarse grain Protein
I did coarse grain simulation of protein (92 residues), the RMSD of the protein is in the range of 1.5 till a small restraints is on the protein beads and as i remove all the restraints (in production).the RMSD shoots up to 6.5 Armstrong . Also I am not able to get back the all-atom structure from coarse grain trajectory , as the secondary structure is completely lost.
Can any one help me with this sudden rise in RMSD and how to reverse bank the coarse grain data to all-atom pdb?
Thanks in Advance
-- -- SUNITA GUPTA
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