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

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 4 16:14:01 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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