[gmx-users] Re: Simulation in the high temperature conditions
Mark.Abraham at anu.edu.au
Mon Apr 9 08:38:11 CEST 2012
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.
> 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
> 4 ?????? 2012 ?. 18:14 ???????????? Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> ???????:
> James Starlight wrote:
> 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 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
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