Re: Colvars Restraint Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Jun 21 2018 - 15:01:39 CDT

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> 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
> 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> 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>
> *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> 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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