Re: Colvars Restraint Question

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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