From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Jun 21 2018 - 15:04:41 CDT
I see, we want to restrain the protein in the bilayer, but not with the restraint on the backbone or alpha carbons, because we
want the protein backbone to be flexible and be able to open up or close during the simulation...
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 2:01:39 PM
To: McGuire, Kelly
Cc: namd-l; Bassam Haddad
Subject: Re: namd-l: Colvars Restraint Question
Oh, I was unaware that dummyAtom was a built-in colvars function - very cool and convenient.
Ultimately the selection you make depends completely on why you want to have a COM restraint. The previous response from Jerome seems to indicate someone who wanted to define another colvar with respect to a frame of reference that they wanted to remain intact. It would seem that covars can do this automatically in many instances without recourse to an additional translational bias.
On Thu, Jun 21, 2018 at 3:53 PM, McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
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<http://www.ks.uiuc.edu>
Re: How to remove center of mass translation of macromolecule. From: Jérôme Hénin (jerome.henin_at_ibpc.fr<http://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<mailto: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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