Re: Re: Re-center membrane protein

From: Ropon-Palacios G. (
Date: Fri May 14 2021 - 12:21:20 CDT

I’m using pbctools,


Following command :  pbc wrap -compound fragment -center com -centersel "protein" -all -shiftcenter {0 1 0}


But bond of atoms crossing pbc box, how fix it bug?


From: <> on behalf of Ramon Mendoza Uriarte <>
Reply-To: <>, Ramon Mendoza Uriarte <>
Date: Friday, May 14, 2021 at 12:19 PM
To: "" <>, "Ropon-Palacios G." <>
Subject: namd-l: Re: Re-center membrane protein


I would suggest looking at VMD's PBCTools Plugin:,can%20be%20used%20within%20VMD%20without%20further%20preparation.

From: <> on behalf of Ropon-Palacios G. <>
Sent: Friday, May 14, 2021 10:02 AM
To: KS UIUC <>
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?.





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