[gmx-users] about heating protocol

Osmany Guirola Cruz osmany.guirola at biocomp.cigb.edu.cu
Mon Feb 7 17:29:25 CET 2011


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?  

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

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

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? 

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

Thanking in advance,

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