[gmx-users] Re: Simulation in the high temperature conditions

Mark Abraham 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
> James
> 4 ?????? 2012 ?. 18:14 ???????????? Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> ???????:
>     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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