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

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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