[gmx-users] Different results with and without constraints for pr coupling.

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 29 19:49:25 CEST 2008

A.Rzepiela wrote:
> Dear all
> 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 freezing.
> 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 
> constraints ?
How about you integration time steps? Could this be induced by some 
strange resonance condition due to too short tau_P, tau_T? Try longer tau_P.
How about the density with and without constraints?
> Andrzej Rzepiela
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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