[gmx-users] Slow-Growth Pressure/System Volume Anomaly
David L. Bostick
dbostick at physics.unc.edu
Wed Dec 5 20:30:26 CET 2001
I am simulating a protein in a hydrated DPPC bilayer. After building the
system and allowing it to come to equilibration, I used the slow-growth
algorithm in order to force one of the dihedrals in the protein to change
from a trans conformation to a cis conformation. I am not interested in
finding the free energy of this conformational change, but I used
slow-growth in order to introduce the change in a somewhat uniform way
throughout a small simulation.
During the run using slow growth, I used anisotropic coupling of pressure
(also used in the equilibration). However, I observe a huge spike in the
system pressure (~0 kJ/mol/nm^3 -> ~4000 kj/mol/nm^3) and
volume (~570nm^3 -> ~770nm^3). I also see a huge rise in the Total Energy
(-5e-5 -> -1.5e-5).
After this perturbation, I imposed the original forcefield again and
eventually, the system pressure, volume, and energy went back to "normal."
I would like someone's opinion on this before I attempt to assign any
physical meaning to this. Is anything in mdrun turned off when using
slow-growth FEP? Can anyone think of any reason for this to occur?
Thanks in advance,
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
More information about the gromacs.org_gmx-users