From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Jun 21 2018 - 13:43:18 CDT
How about in the colvars file though where I select two groups, one being the center of mass for the
protein-bilayer system and then a dummy atom...? In the group with the lipids/protein, would I just
list all of the serial atom numbers or residue names...?
Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: Bassam Haddad <bhaddad_at_pdx.edu>
Sent: Thursday, June 21, 2018 11:33:58 AM
To: namd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: Re: namd-l: Colvars Restraint Question
Hi Kelly,
I think your atom selection in vmd would be...
set sel [atomselect top "lipids or protein"]
Bassam
On Thu, Jun 21, 2018 at 10:05 AM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
I would like to place a harmonic restraint on the center of mass of a protein-membrane system. I have an ion channel
in a bilayer, and I would like to restrain the COM of that system during my adaptive biasing force simulation. What would
the atom selection look like in order to create that restraint?
Kelly L. McGuire
PhD Scholar
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
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