[gmx-users] Re:total energy

[Nuno R. L. Ferreira]

Hi Lakshmi

>    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.
David just answered this one.

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

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


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

For example:

ref_t=500
annealing=yes
zero_temp_time=1000
nsteps=500000
dt=0.002

will cool down your system from 500 k to 0k in 1ns

Check the manual, the mail list and some articles about SA.

Regards,
Nuno


#######
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal

Phone: +351 239 852080
Fax: +351 239 827703
www.biolchem.qui.uc.pt
####