[gmx-users] about heating protocol

[Justin A. Lemkul]

Osmany Guirola Cruz wrote:
> Hi,
> 
> As I haven seen in many papers regarding molecular dynamics and in
> particular, using the Gromacs software, it seems a common feature to do
> a gradually increase of temperature previous to do the final production
> run. I noted that some researches do not use simulating annealing
> algorithm to do heating, but I did not figure out if they use position
> restrained runs or short production runs.
> 
> I would really appreciate, if you could answer the following questions
> and also your give a point of view regarding the relevance of the
> heating process for the final dynamic simulations results. 
> 
> 1. Does the omitting of the heating process will give wrong results?  
> 

No.

> 2. Does a production run at 300K necessarily requires to do a previous
> heating process?
> 

No, but you need sufficient equilibration under the desired conditions.

> 3. The heating process is only recommend when production runs are done
> for higher temperatures, for instance 373 K?
> 

Not necessarily, but it is more common in these cases, I believe.

> 4. The heating process is done running several position restrained at
> different temperature values (for example, every 50 K) previous to do
> the finally production run? 
> 

I don't quite follow you here.  Position restraints are generally applied during 
any initial equilibration, independent of whether or not annealing is applied. 
Some basic textbook reading would explain the underlying methodology.

> 5. The heating process is done running short production runs at
> different temperatures values?
> 

Heating is done by simulated annealing.  You can specify plateau regions wherein 
the temperature is held constant prior to any subsequent increase or decrease in 
temperature.  There is an example in the manual.

-Justin

> Thanking in advance,
> Osmany
> 
> 

-- 
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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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