On 9/04/2012 4:18 PM, James Starlight wrote:
By the way I've completed equilibration phase of my system ( receptor
in Ccl4-water membrane mimicking layer) in the hight temperature
conditions. :)
During 3ns I gradually increased temperature from 300 to 700k with
posres applied on the Ccl4 C atoms and all atoms of protein. After
this I've changed posres applied on the protein to the backbone atoms
only and started gradually decrease fc falue ( from 1000 to 250 ). The
overal system was stabile and I've noticed linnear increase of the
total energy accompanied by such increase of temperature.
Than When I've removed posres from side-chains I've noticed bigger
RMSD in potential energy of my system.
The only artifact that I've noticed is that some water was moved into
the Ccl4 layer during this equilibration. How I could prevent such
layer mixing without applying posres on water?
I doubt you can. If you make your layer boundaries perpendicular to some
axis then you can use position restraints on water oxygens that have
non-zero force constants only with respect to that axis. Then relax the
water position restraints before any others.
I need free-water in my system because I want to see how some water
move into the receptor that have a chanell wich some internal- water
cavities having functional meaning.
That doesn't stop you restraining water during equilibration.
Does some operation with the COM option could prevent mixing of some
differen solvent layers ?
Doing anything to COM of any group of many molecules is not going to
prevent one molecule from diffusing across a boundary.
Mark
At the curent moment I've difined COM as
Protein_CCl4 SOL_NA_CL_XW
where XW is the water observed in the X-ray structure of that protein
( I've defined that mollecules in separate layer)
Thanks for help
James
4 ?????? 2012 ?. 18:14 ???????????? Justin A. Lemkul <[email protected]
<mailto:[email protected]>> ???????:
James Starlight wrote:
Justin,
1) I've defined 5 steps for specified definition of the time
of each step as well as for more flexibile controle of the
such annealing: e.g I want that equilibration step
corresponded to the temperature between 320 and 330K will be
longer than between first step corresponded to 300-310K etc
OK, that makes sense. What you showed before does not do that,
hence my confusion.
2) About velosities. As I understood for annealing
equilibration gen_temp must be equal to the starting
temperature of such equilibration ( gen_temp= 300 in the above
example). But in what exactly circumstances the changing in
gen_temp could be usefull? As I've told after such annealing
equilibration I want to simulate my system on the high
temperature condition for efficient conformation sampling.
Might it be that initial high velocities could be usefull for
such sampling efficacy?
I'm not clear on what you're asking. If you are generating
velocities (which you wouldn't after you reach your target via SA
or equilibration), then you don't need gen_temp or gen_vel. If
you're starting a new run, then gen_temp should be equal to the
ref_t value you wish to use for the simulation. If your gen_temp
and ref_t values are not the same, then it is quite possible that
the simulation will crash or give very unexpected results due to
potential instabilities in the thermostat algorithm.
-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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