Re: to rigidify bonds without hydrogen (about suggestion

From: zeynab hosseini (
Date: Mon Aug 29 2022 - 06:38:56 CDT

Hi Norman,

Thank you so much for the prompt reply. I want to rigid all bonds in SiC
and then performing Steered MD on the mass center of the nanotube and move
that. I assume in this case it is not possible to use fixedatoms option as
it constrains the atoms to the initial position and does not let them move
during the SMD.

All the best,

On Mon, Aug 29, 2022 at 3:41 PM Geist, Norman <> wrote:

> If you really wanna change Molecule.c you'd have to recompile NAMD from
> source. This isn't usually as difficult given a comprehensive description
> in "notes.txt" shipped with the NAMD source code.
> Bests
> Norman Geist
> Am Montag, den 29-08-2022 um 12:59 schrieb zeynab hosseini:
> Dear all,
> I want to rigidify all covalent bonds in a Silicon Carbide (SiC) nanotube.
> I'm following the suggestion below which is used for MARTINI simulation in
> NAMD. I wonder if this suggestion can work in my case which includes 4
> bonds for each atom to rigidify.
> <;!!DZ3fjg!_jyIpnZoICdzrlUpkVJpWAJ97P95kFKbHDOmdZQwIWC-j1yLM12y7z2rcycrLeRtdcH4SSlE4q__k4zA5HgW6sMM_dWM$>
> Maybe stupid questien as I'm not familiar with the source code stuffs: I
> found "Molecule.C" file in the NAMD source code. I wonder after modifying
> the Molecule.C I have to compile the source code to get it to work? Since I
> always used to install the compiled version of NAMD.
> All the best,
> Zeynab

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST