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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