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

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 10 14:21:15 CEST 2012

James Starlight wrote:
> Justin,
> Could you tell me for what purposes the definition of the several ref_t 
> values could be usefull? Does this just for measurements of the 
> temperature during simulation for each group separately or is there 
> something else?

Each ref_t value is the target temperature for however many groups you have 
assigned to separate thermostats.

> By the way as I've found in literature another important question about 
> such simulation in high temperature conditions is the selection of the 
> integrator algorithm wich also could enhanse sampling under this 
> conditions.  E.g I've found that the BD integrator could be more usefull 
> than leap-frog MD. What timestep and other importnat options defined in 
> mdp should be tken into account within simulation with BD ? I've never 
> perform simulations with this integrator and could not realise how it 
> could enhanse simulation rate in comparison to the MD and what artifacts 
> should expect from that :)

I have never used the bd integrator so I cannot offer any help here.  I don't 
see any magical reason why you should expect it to enhance sampling though.



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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