Re: Colvars Restraint Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Jun 21 2018 - 14:53:17 CDT

Hmmm, I was going off of this response in the mailing list, this is where I got the idea for the

dummy atom:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/0768.html

namd-l: Re: How to remove center of mass translation of ...<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/0768.html>
www.ks.uiuc.edu
Re: How to remove center of mass translation of macromolecule. From: Jérôme Hénin (jerome.henin_at_ibpc.fr) Date: Wed Jun 12 2013 - 04:00:48 CDT Next message: Shubhra Ghosh Dastidar: "Error while running the infiniband version."

I was worried though that I would have to type every serial atom number for the membrane and protein into one of

the groups...

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Brian Radak <brian.radak_at_gmail.com>
Sent: Thursday, June 21, 2018 1:01:23 PM
To: namd-l; McGuire, Kelly
Cc: Bassam Haddad
Subject: Re: namd-l: Colvars Restraint Question

This should be pretty clear from the user's guide.

Harmonic center of mass restraints operate on a scalar distance. The first group is not anchored to a fixed point but rather to another point defined by another group. I don't know the standard practice, but defining group 2 as a dummy atom experiencing no forces and with no velocity would constitute a fixed point. Maybe use fixedAtoms?

Also, you should generally keep center of mass selections as small as possible for performance purposes.

On Thu, Jun 21, 2018 at 2:43 PM, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

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<mailto:bhaddad_at_pdx.edu>>
Sent: Thursday, June 21, 2018 11:33:58 AM
To: namd-l_at_ks.uiuc.edu<mailto: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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