From: Shahee Islam (
Date: Mon Dec 04 2017 - 03:57:36 CST

Thank you so much for your reply.But after doing this the two proteins
remains at the center of the water box,but the interface between the two
proteins change with the progressing of the time of the trajectory.due to
this there will be problem in the analysis of the contract between the two
proteins,the distance between the center of geometry of the two protein.Is
there any solution where the two proteins will remain in the box and their
faces will not change.

thanking you
Shahee Islam
university of calcutta
department of chemistry

On Fri, Dec 1, 2017 at 8:05 PM, Vermaas, Joshua <>

> 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 <<mailto:
>>> wrote:
> Hi
> 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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:43 CST