[gmx-users] Different results with and without constraints for pr coupling.
A.Rzepiela at rug.nl
Fri Aug 29 15:39:02 CEST 2008
The system, 75 hexadecane molecules, when simulated with
Parrinello-Rahman (isotropic), Nose-Hoover and option "constraints
= none" is freezing. When constraints are changed to "constraints
= all-bonds" (lincs), this is not observed ( temp is above
melting point ). This behavior does not depend on tau_p value (
checked for 0.5 and 2 ) and is probably not connected to nose-hoover.
When simulation is carried with nose-hoover and berendsen pressure
coupling, freezing with all-bonds option is not observed . Also when
berendsen temp. and pressure coupling is applied system is not
Starting structure was equilibrated with berendsen coupling, freezing
starts after few hundred picoseconds. After that average pressure and
temperature is correct, but fluctuations are very high. Bonded
potential energy increases a few times, the rest drop down.
Simulations were done with gromacs3.3.1, 3.3.3 and CVS version
What can be the reason for different behavior with and without
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