[gmx-users] freeze group

[Justin A. Lemkul]

subarna thakur wrote:
> I running the simulation of a protein with Fe4s4 cluster. The parameters 
> for the cluster were obtained from a previously published paper. I have 
> been able to carry out energy minimization with the following keywords-

<snip>

> *a) Can I freeze the movement of the Fe4S4 cluster during simulation by 
> incorporating the cluster in freeze group?*
> 

"Can I?" and "should I?" are separate concepts.  Of course you can, but would 
that be useful?  See below.

> *b) If yes, then how do I incorporate the freeze group in Pr.mdp file 
> during position restraining step?*
> 

Please read the manual.

> *c) Is there any other alternative to correct the linc warning error?*
> 

I would suggest several things before trying to freeze the cluster artificially. 
  First, choose a more stringent energy minimization criterion.  Fmax < 2000 is 
typically insufficient for almost any system.  Also, having the cluster as its 
own separate temperature coupling group is inappropriate.  See here, 
specifically the second point under "What Not To Do":

http://www.gromacs.org/Documentation/Terminology/Thermostats

-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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