Re: to rigidify bonds without hydrogen (about suggestion

From: Geist, Norman (
Date: Mon Aug 29 2022 - 06:11:32 CDT

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.

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)
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!-bBzkn6JB71VoExlylMqXrbvQKpROZk9Wsat-7SkzC8TsaVD8SIK6QgeWbCEnFY4sPCq0J1DN3Uks7KtKYlJ0WlFbTjOkMNVrQ$ [1]

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,


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