On 19/04/2012 4:55 PM, James Starlight wrote:
Justin,
I've tested default disres applied to my protein under high
temperature condiitions.
I've observed that default disre_dist as well as its values up to 0.3
nm in general prevent destabilisation of my protein under non-native
conditions allowing some dynamics of the restrained regions ( I've not
used disre_frac in all this experiments). But starting from the values
of 0.5 nm my protein was perturbed again.
So the remained questions are
1) Firstly I'd like to test different cutoff radii for the
increasing\decreasing number of disres but I didnt know how exactly
define this value more accuracy ( previously I've used such cutoff
radius for normal mode analysis of such protein ( in thact case Rc
define contacts between C-alpha atoms ) where the value of 0.8-1 nm
gave me good results).
2) My protein consist of some internal water mollecules wich I've
defined explicitly as the separate group (I've coppied coordinates of
such waters from the X-ray structure ). During dynamics RUN I've
noticed that some of this waters were moved out from receptor to the
SOL layer and only several waters remined in the bounded state with
the interoiour of my protein.
Diffusion in and out of receptors is physical - you may not want to
prevent that. At high temperatures the rate of diffusion will increase,
and this is yet another problem with your attempted approach.
How I could specify T_couple and COM groups for such internal waters
most accyracy?
COM removal is not for preventing a group of atoms from moving. Maybe a
COM virtual site with a position restraint would achieve that, but if
you really need to keep some water in the receptor, you need to put
position restraints on those waters (and pray that your results mean
something and people have a reason to believe you).
Mark
I've tried to define it as the part of SOL_Ions layer as well as in
the common group with the protein for both the T_coupling and COM but
I have not noticed any difference between that simulations.
Thanks for help again,
James
16 ?????? 2012 ?. 18:09 ???????????? Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> ???????:
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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