[gmx-users] constraints and PME options

[David van der Spoel]

On Tue, 2005-05-24 at 12:10 +0800, Jian Zou wrote:
> Hi all,
> 
> My system is a chaged protein in water.
> when doing the full md simulation after PR-md, I'm not sure about several 
> mdp options.
> 
> 1. how should I choose the "constraints=no" or "constaints=all-bonds"? 
> What's the difference between them according to my system? What about 
> "constaints=hbonds"?
Usually you want constraints = all-bonds
since it allow a time step of 2 fs. See chapter 1 and 3 of the manual.

> 
> 2. I use PME, but I don't really know how to set the values for 
> "fourierspacing" and "pme_order".
> In previous discussion (2004-06), someone posted a comparison, like
> (1) Ewald with fourier_nx = 4: stddev = 1.06
> (2) Ewald with fourier_nx = 5: stddev = 0.068
> (3) PME with fourierspacing = 0.1, interpolation order 6: stddev = 0.33
> (4) PME with fourierspacing = 0.12, interpolation order 6: stddev = 1.27
> (5) PME with fourierspacing = 0.12, interpolation order 4: stddev = 4.07
> What about the simulation time needed for different combinations?
> I want to use
> "fourierspacing=0.12" "pme_order=4",
> or "fourierspacing=0.12" "pme_order=6",
> or "fourierspacing=0.1" "pme_order=4"
> Which is more suitable for my case?

My favorite is the latter. 0.1/4.


> 
> Thanks in advance for your advice and comments.
> 
> 
> Regards,
> 
> Jian Zou
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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