Re: SMD: Fixing centroid

From: Jérôme Hénin (
Date: Tue Dec 14 2021 - 08:10:25 CST

Hi all,

Adding to the answer by Anup: if you pull on a distance colvar, there is probably no need for fixing (or restraining) any group of atoms. However, if you want to pull along a specific direction, you can use the "distanceZ" function, specifying that the axis is not z but x.


----- On 14 Déc 21, at 12:02, Anup Prasad <> wrote:

> Hi Dr. Moumita,
> I don't think that there is any straightforward command for fixing the centroid
> of a group of atoms. Instead of it you can try the "distance colvar" module.
> You have to calculate the centre of mass (com) of the group of atoms and create
> the dummy atom at this com. Then apply distance colvar between "group of atoms"
> and "dummy atoms" along with SMD simulation. Fix the dummy atom in SMD instead
> of a group of atoms.

> [ |
> ]

> Cheers
> Anup

> On Tue, 14 Dec 2021 at 15:52, Moumita Saharay < [
> | ] > wrote:

>> Dear all,
>> I want to perform a constant velocity pulling experiment using
>> Steered Molecular Dynamics (SMD). I used the following TCL
>> script to mark the fixed and SMD atoms. It works well when there is
>> only one atom to be fixed. But I want to fix the centroid of a collection of
>> CA atoms, for example, CA atoms of GLU203, PHE257, and ASP480.
>> How do I do that ? Please help me to resolve this issue.

>> TCL script:
>> set allatoms [atomselect top all]
>> $allatoms set beta 0
>> set fixedatom [atomselect top "resname GLU and resid 203 and name CA"]
>> $fixedatom set beta 1
>> $allatoms set occupancy 0
>> set smdatom [atomselect top "index 10525"]
>> $smdatom set occupancy 1
>> $allatoms writepdb smd_step5_01.ref
>> set smdpos [lindex [$smdatom get {x y z}] 0]
>> set fixedpos [lindex [$fixedatom get {x y z}] 0]
>> vecnorm [vecsub $smdpos $fixedpos]

>> Thanks,
>> Moumita
>> --
>> Dr. Moumita Saharay
>> Assistant Professor,
>> Department of Systems and Computational Biology,
>> School of Life Sciences,
>> University of Hyderabad,
>> Gachibowli, Hyderabad, India

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST