[gmx-users] Using the Berendsen Barostat to Initialize and then switch to Parrinello-Rahman

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 30 20:00:42 CEST 2010

Andrew Mauro wrote:
> Hello all,
> I have a system that I am trying to get to one bar pressure in an NPT 
> and then use the average volume to determine the box size for my NVT 
> simulation.  I want to use the Berendsen barostat to get my pressure 
> close and then use the Parrinello-Rahman to have the correct ensemble 
> with which to determine the proper box size.
> I've tried appending the energy file by using grompp -e *.edr and this 
> yields the error Missing energy term Box_Vel_XX.  There's a good chance 
> that I'm approaching this wrong but any help in specifying how to 
> properly continue would be greatly appreciated.

Don't use the .edr file.  Pass a checkpoint file to -t to continue.  If you're 
switching thermostats or barostats, the .edr file will not have the right 
information.  The best thing is to use the .cpt to maintain proper velocities, 
etc since there will not be any coupling information for the new barostat algorithm.


> -- 
> Andrew Mauro


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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