restraint

LAMMPS LAMMPS Mailing List Mirror
1

Dear Experts

I have a self-assembly of flavin nucleotides that form a helix around a carbon nanotube. I placed the system in such a way that the axis of the nanotube is the z-axis. I constructed the flavins in such a way they are aligned with the z axis. Upon minimization flavins tend to tilt and obtain an epitaxial orientation with respect to the nanotube. Is there a way in lammps where I can force the flavins to stay aligned with to z-axis upon minimization. I attached a illustration.

Best

Milinda Samaraweera
Computational materials chemistry and Computer programming
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA

tilt.jpg

2

Dear Experts

I have a self-assembly of flavin nucleotides that form a helix around a
carbon nanotube. I placed the system in such a way that the axis of the
nanotube is the z-axis. I constructed the flavins in such a way they are
aligned with the z axis. Upon minimization flavins tend to tilt and obtain
an epitaxial orientation with respect to the nanotube. Is there a way in
lammps where I can force the flavins to stay aligned with to z-axis upon
minimization. I attached a illustration.

please check out fix colvars, which allows many kinds of different restraints.

axel.

3

Hi Axel

I tried building /lib/colvars using

make -f Makefile.g++

but I dont get the 
  
libcolvars.a

How to build it correctly

Best
Milinda

Milinda Samaraweera
Computational materials chemistry and Computer programming
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA

Dear Experts

I have a self-assembly of flavin nucleotides that form a helix around a
carbon nanotube. I placed the system in such a way that the axis of the
nanotube is the z-axis. I constructed the flavins in such a way they are
aligned with the z axis. Upon minimization flavins tend to tilt and obtain
an epitaxial orientation with respect to the nanotube. Is there a way in
lammps where I can force the flavins to stay aligned with to z-axis upon
minimization. I attached a illustration.

please check out fix colvars, which allows many kinds of different restraints.

axel.

4

Hi Axel

I tried building /lib/colvars using

make -f Makefile.g++

but I dont get the

libcolvars.a

How to build it correctly

exactly like it says in the documentation. if it doesn't work, there
have to be error messages and i cannot read them from here.

axel.