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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 16 16:09:12 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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