From: Vermaas, Joshua (
Date: Fri Dec 01 2017 - 08:35:31 CST

In the future, just only turn wrapwater on, not wrapall. For your current conundrum, you can use pbctools to rewrap the system using an atomselection at the interface as the center of the selection.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory<>

On Dec 1, 2017, at 1:28 AM, Shahee Islam <<>> wrote:

I am doing simulation of two proteins system in namd.But after 150 ns of the simulation one protein is going away from the another protein due to pbc.After this i have done recentreing of the proteins but having problem during the analysis(by charmm) of distance between the centre of geometry of the two proteins as part of a one protein is on the opposite parallel face of the box.
Water box size 73.0 72.0 72.0
Protein size 30.42 31.75 31.30(measure from vmd)
Thanking you

Shahee Islam
University of calcutta
department of chemistry

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