Wrapping molecules in a NAMD simulation

From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Apr 04 2016 - 08:23:02 CDT


I am trying to replicate the aggregation of four coarse-grained peptides.
Although during the course of simulation, I observe a trimer formation at
the *box edge*, but one of the peptides is sometimes attached and sometimes
not to the trimer when the coordinates are wrapped. Although after
unwrapping, the trimer is no longer there. My questions are:

1. Is the trimer formation occurring or not in the simulation?
2. Are the interpeptide distances calculated from the unwrapped coordinates
correct or do they need alteration on the account of the minimum image
3. Can I remove the COMmotion selectively for the four peptide molecules?

I am using the pbc command below to unwrap the peptide molecules:

pbc unwrap -sel "segname P1 P2 P3 P4"

Thanks and regards

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