Re: to rigidify bonds without hydrogen (about suggestion

From: Geist, Norman (
Date: Mon Aug 29 2022 - 06:09:21 CDT


in case fixing all bond lengths would do the same as freezing the
atoms, you could potentially use "fixedatoms" instead.

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!4IZheiLsXR2YCQv3kktclmKKHxGjU9omKITQ4K8tGHc9lHVSBI79En6x_EZjsaMIQ4qKZ5JcIIh600Y1RuUOvUaWiU0vcZ0sng$ [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,


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