[gmx-users] Re: Re: NPT simulation with parinello-rahman pressure coupling

[Justin A. Lemkul]

Shyno Mathew wrote:
> Hello Justin,
> Thanks for your reply.
> 
> Yes, absolutely.  The Berendsen method leads to faster convergence, while 
> Parrinello-Rahman often fluctuates to a larger extent before settling around the 
> target pressure values.  It is not suitable for equilibration, generally.  Have 
> 
> you done prior equilibration for this system?
> 
> Actually, this run is an equilibration. So I guess for pressure 
> coupling, it is good to use Berendsen for equilibration rather than PR?
> 

Yes.

> Also note that you're not providing several important parameters in your 
> 
> pressure coupling section, like reference pressures and compressibilities.  With 
> anisotropic pressure coupling, you should make sure that the off-diagonal 
> components are not causing compression or distortion of your system, as the 
> 
> manual advises.
> 
> Yes, these parameters are there in the .mdp file (as shown below), in 
> the previous email, I didn't include them.
> pcoupl                   = Parrinello-Rahman
> pcoupltype               = anisotropic
> nstpcouple               = -1
> tau_p                    = 1.0
> compressibility          = 4.6e-5 4.6e-5 4.6e-5 0 0 0
> ref_p                    = 1.0 1.0 1.0 0.0 0.0 0.0
> 

Always make sure to include full information.  It will help us figure out 
potential problems faster, rather than guess, which then gets you a resolution 
faster ;)

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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