[gmx-users] Re: Simulation in the high temperature conditions

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> 
> Thank you for explanation. Tomorrow I'll try to check results of 
> simulation with the disres applied with its default values as well as 
> with narrower -disre_dist values ( ignorring -disre_frac option at all 
> )  and post here results of such simulations.
> 
> 
> 1) The cut-off distance wich I've specified was defined with the genrest 
> comand with the -cutoff 1.0 flag. Finally all restrains were apllied on 
> the backbone atoms of alpha helices of the Transmembrane domain of my 
> protein wich I've defined in the index.ndx file. So all loops of my 
> protein were not-restrained at all.
> 

Ah, I see now.

> Also I have some small  question about size of output edr file. I've 
> noticed that size of this files of such simulations  (with the disres 
> applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why 
> this occurs and how I could fix it?
> 
> 

There are energy terms associated with distance restraints.  They cause the .edr 
file to get large very fast if you have a lot of them.  You'll have to decrease 
nstenergy to make the files smaller, or not use the restraints.

-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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