VMD-L Mailing List

From: Georgia Tsagkaropoulou (georgiatsagaropoulou_at_gmail.com)
Date: Wed Dec 09 2015 - 11:19:25 CST

Hello everyone,

I have a question which is connected to both LAMMPS and VMD

: I am trying to simulate some long molecules ( consisting of C,O and H) in
an NPT ensemble, to observe some conformational changes. However, I get the
message of missing bonds or atoms in dihedrals and my simulation crashes
in maximum 100.000 femtoseconds.

I have looked up the relevant solutions ( fix/nve, fix langevin, and I use
a small timestep of 0.1). The missing atoms are due to atom overlap , which
causes an abnormally high temperature and eventually one of the atoms gets
blown out of the box.

My coefficients are correct - I have double-checked them. I use packmol to
pack around 30 molecules and then VMD with the topo tools to assign charges
etc.

When I first view the molecules in the VMD (prior to lammps), the structure
is correct. However when I see in VMD the trajectory of the lammps file ,
until it crashes, the molecules seem to not have some bonds and have
created others, despite the fact that the VMD displayed them correctly in
the first place.

I know it is not a LAMMPS issue because i did the exact same simulations
with a similar molecule and it worked perfectly. So I think it is a VMD
issue that I am having. Is it possible that the radii of the atoms are not
correct, even though the display is correct? For example, for carbon, a
radius of either 1.4 or 1.3 Angstrom leads to a correct display, but maybe
the lower value can lead to overlap...?

Thank you for your time!
Georgia