[gmx-users] total energy

[Anton Feenstra]

Lakshmi Padmavathi wrote:

> Dear Gromcas users,
>     
>     i am simulating an system with distance restriants. the total energy of 
> the system is 5*10^5(ex: 581219).
> 1.How can i get my system to its minimum energy.

Energy minimization! (integrator=steep in you mdp file)

> 2. if i do simulated annealing, am i need to do it with energy minimisation or 
> with md run.

There is no such thing as temperature in EM, so you need MD in SA.

> 3. in simulated annealing once the temp coming down to 0k (zero_temp_time), 
> the system is not heating again.

Although this is not a question, I will give an answer anyway ;-)
If you want to heat, you must start a new simulation using the final coordinates
of the cooling one as the starting point and set zero_temp_time negative ( <0 ).

> 4. what should i do for slow cooling ( some of the mail list says that slow 
> cooling is better.

Increase zero_temp_time.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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