Re: restraining selected atom's z coordinates

From: Vermaas, Joshua (
Date: Mon May 15 2017 - 11:30:55 CDT

Alternatively, you can also tag specific atoms and then use the normal harmonic restraint stuff. So in VMD, it would be:

set allsel [atomselect top "all"]
$allsel set beta 0
set restrainsel [atomselect top "name C21 C31"]
$restrainsel set beta 1
$allsel writepdb tag.pdb

And then in NAMD do as follows:

contraints on
consref tag.pdb
conskfile tag.pdb
conskcol B
selectConstraints on
selectConstrZ on

Combined, this will apply a hamonic potential with a 1kcal/mol/Angstrom^2 force constant to the C21 and C31 atoms to restrain them to their initial positions in the pdb.

On 05/14/2017 12:59 AM, Ajasja Ljubeti wrote:

sure, I think distanceZ<> colvar should fit your needs.


On 14 May 2017 at 02:17, Rabeta Yeasmin <<>> wrote:

I want to constrain z coordinates of some selected atoms. The NAMD user manual showed one option which is for restraing the z coordinates for all atoms. Can anyone please tell me if there is any way to restrain selected atoms z coordinates?

Rabeta Yeasmin

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