Re: Colvars Restraint Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Jun 21 2018 - 14:01:23 CDT

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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