Re: Re-center membrane protein

From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Fri May 14 2021 - 12:18:13 CDT

I would suggest looking at VMD's PBCTools Plugin:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#:~:text=Since%20VMD%20version%201.8.6%2C%20the%20PBCTools%20plugin%20is,can%20be%20used%20within%20VMD%20without%20further%20preparation.
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Ropon-Palacios G. <biodano.geo_at_gmail.com>
Sent: Friday, May 14, 2021 10:02 AM
To: KS UIUC <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Re-center membrane protein

Hello namd users,

I am running a simulation of a protein in membrane, which after 200 ns of simulation goes to a corner of the membrane and stays there for a long time, I want to perform the analyzes and I want to put it back in the center, how could I do this, without the links crossing the pbc box?.

Best,

Geo.

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