[gmx-users] System size increases and exceeds unit cell dimensions during simulation.

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Thu Apr 2 19:05:39 CEST 2015

Hi Everyone,
I am trying to make a bilayer system composed of oil (triglyceride) and
water. While energy minimization and subsequent step (NVT and NPT) some of
the lipid molecules are going out of the unit cell and hence the system
size (as measured by editconf) increases, however the unit cell size as
mentioned in output.gro doesn't change. As per my knowledge if a molecule
(or part of the molecule) goes out through one face should appear through
opposite face, but this isn't happening. During my early simulation (only
lipid without water phase) I have observed fragmented molecules near the
borders ( part of the molecule that goes out through one face, appears
through opposite face) which I think is normal. But I don't know why after
adding water layer I am getting this problem. Following is the relevant
lines in mdout.mdp file, which is same as earlier.

; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic-molecules       = no

Any suggestion is most welcome.

Thanks for your valuable time and suggestion.
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

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