[gmx-users] pressure problems

[Marcelo Müller]

Hello gmx users,

I've got some problems about pressure scaling and box shift at the beginning of a simulation.
I'm simulating the md of a protein in a cubic box with TIP3P water (0.9 nm to the box side). Firstly, I've done a energy minimization applying steepest descent and conjugate gradient algorithms. The system was neutralised adding two Na+ and a energy minimisation was again done. After, the system was equilibrated  during 1 ns at 300K (Berendsen thermostat was on)  and 1 atm (Parrinello-Rahman  pressure coupling was on).
When, I start the md simulation a message of error returns - box was shifted more than 10 times. When I turn off the pressure coupling everything is all right.
Do you have some idea about this problem?
Thank you,

Marcelo


Marcelo Müller dos Santos, Ph.D. student
Laboratorio de Tecnologia Enzimatica e Biocatalise
Departamento de Bioquimica e Biologia Molecular, Setor de Ciencias Biologicas, Centro Politecnico, Jardim da Américas, Curitiba - PR, Caixa Postal: 190-46, CEP: 81531-990
Phone: (+55) 41 3361-1658
Fax: (+55) 41 3266-2042 
_________________________________________________________________
Cansado de espaço para só 50 fotos? Conheça o Spaces, o site de relacionamentos com até 6,000 fotos!
http://www.amigosdomessenger.com.br
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080527/07800bb4/attachment.html>