[gmx-users] constraints and PME options

[Jian Zou]

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"?

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?

Thanks in advance for your advice and comments.


Regards,

Jian Zou