Erratic pressure values during equilibration of water box

From: Ashwin C.V. (
Date: Sun Jun 17 2012 - 08:49:27 CDT

In our learning process,we were trying to run minimization and
equilibration on a simple water box system using NPT ensemble.We used
Berendsen Pressure bath coupling as follows.
*BerendsenPressure on
BerendsenPressureTarget 1.01325
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 20
BerendsenPressureFreq 2*

Also for achieving constant temperature we used langevin dynamics as follows

*langevin on
langevinTemp 300
langevinDamping 5

*After running for about 100,000 time steps of 1fs each,we observed that
the output pressure values from namd was always fluctuating between -100
bar and +100 bar.Also after increasing no of time steps,we were not able to
get a convergence zone neither a constant value.
When we read other questions on the mailing list some of it pointed to the
fact that these fluctuations between lower and upper bounds were acceptable.
Is it possible in any way to achieve a convergence zone and constant
pressure at the end of equilibration?
Undergraduate student
National Institute Of Technology-Trichy

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:40 CST