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On 19/04/2012 4:55 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopwKRxtuXGhfG_J=N14Fh=9QuMFGhHTpTs_raxsyzVvmLg@mail.gmail.com"
type="cite">Justin,<br>
<br>
<br>
I've tested default disres applied to my protein under high
temperature condiitions.<br>
<br>
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.<br>
<br>
So the remained questions are<br>
<br>
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).<br>
<br>
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.</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAALQopwKRxtuXGhfG_J=N14Fh=9QuMFGhHTpTs_raxsyzVvmLg@mail.gmail.com"
type="cite"> How I could specify T_couple and COM groups for such
internal waters most accyracy?</blockquote>
<br>
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).<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopwKRxtuXGhfG_J=N14Fh=9QuMFGhHTpTs_raxsyzVvmLg@mail.gmail.com"
type="cite"> 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. <br>
<br>
<br>
Thanks for help again,<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">16 апреля 2012 г. 18:09 пользователь
Justin A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
<br>
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.<br>
<br>
<br>
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.<br>
<br>
</blockquote>
<br>
</div>
Ah, I see now.
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
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?<br>
<br>
<br>
</blockquote>
<br>
</div>
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.
<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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