[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
--
========================================
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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