[gmx-users] Simulated Annealing

[Anton Feenstra]

Shang-Te Danny Hsu wrote:
> 
> Hi there,
> 
> I am trying to perform Simulated Annealing protocol by GROMACS3.0. I
> simply adopted the runfile *.mdp from my previous simulation at constant
> temperature by adding:
> 
> ; Simulated Annealing
> annealing = yes
> zero_temp_time = -1000
> 
> Negative zero_temp_time is to heat up the system. Then the system blows
> up at step0 with lots of bond length violation. The system has been
> first energy minimized and released for dynamics for 100ps in water.
> Should be more or less stable. What are the possibilities to fix this
> problem?

Don't know. First thing I would check is to get your original .mdp
file and generate a .tpr file with that. Than change to your 'annealing'
.mdp file and generate another .tpr file, keeping all other things
(i.e. .gro/.pdb and .top) identical. Then you can compare both .tpr
files using 'gmxcheck -s1 normal.tpr -s2 anneal.tpr'. That will tell
you whether you really changed what you think you did...

-- 
Groetjes,

Anton
 ________ __________________________________________________________
|        | Anton Feenstra                                           |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam   |
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| ' __   | Feenstra at chem.vu.nl - www.chem.vu.nl/afdelingen/FAR      |
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