Re: Re: Re-center membrane protein

From: Ropon-Palacios G. (biodano.geo_at_gmail.com)
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: <owner-namd-l_at_ks.uiuc.edu> on behalf of Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
Reply-To: <namd-l_at_ks.uiuc.edu>, Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
Date: Friday, May 14, 2021 at 12:19 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo_at_gmail.com>
Subject: namd-l: Re: Re-center membrane protein

 

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.

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST