Re: Re: Re-center membrane protein

From: Ramon Mendoza Uriarte (
Date: Fri May 14 2021 - 12:51:41 CDT

For the future use the VMD mailing list for VMD related questions.

You can maybe try a different center first and then com:

pbc wrap -all -compound fragment -center origin
pbc wrap -all -compound fragment -center com -centersel "protein"
From: Ropon-Palacios G. <>
Sent: Friday, May 14, 2021 10:21 AM
To: <>; Ramon Mendoza Uriarte <>
Subject: Re: namd-l: Re: Re-center membrane protein

Iím 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.s/pbctools/*:*:text=Since*20VMD*20version*201.8.6*2C*20the*20PBCTools*20plugin*20is,can*20be*20used*20within*20VMD*20without*20further*20preparation.__;I34lJSUlJSUlJSUlJSUlJSU!!BpyFHLRN4TMTrA!pV7zoCU5pUR4iqAHL3-T1Ogqk5IkRgtn7XSkacAayzACf9R4fDEKOmmQ-kmXqvYGhbPL$>


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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