[gmx-users] "freezegrps" concept

[Justin A. Lemkul]

YUVRAJ UBOVEJA wrote:
> Hello
> 
> I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen 
> "cubic" as box with distance of 1nm b/w solute n box.
> Protein is going out of the box after equilibration step. Any solution?
> 

FAQ #11.

http://www.gromacs.org/Documentation/FAQs

Please also note that if you search for a generic phrase like "protein out of 
box" on the mailing list archive, your answer will turn up as the first post 
(and then several hundred more).

> Should i use *freezegrps* option to restrict protein movement. Please 
> provide some light to this option. What effect it will have on the whole 
> system?
> 

If you're trying to fit the position of the protein into some preconceived 
notion of what it should be doing, stop.  If you are trying to appropriately 
equilibrate the solvent while keeping the protein fixed (in any arbitrary 
location), position restraints are much easier because:

1. They are already present in the topology and are easily invoked
2. Freezing is incompatible with pressure coupling
3. If proper energygrp_excl are not used, you can end up generating very large 
forces

-Justin

> -- 
> Yuvraj
> 

-- 
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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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