[gmx-users] Simulated annealing 10000K

[Kay Gottschalk]

At 10000K you can only do torsion angle dynamics, I think. Your box is 
just exploding. I am not sure that you will find a sa scheme with which 
your peptide models  converge. Do you have any experimental restraints? 
How big is the peptide?
On Thursday, July 31, 2003, at 01:07 AM, Osmany Guirola Cruz wrote:

> At  10000K my simulation does not work  i have errors like this.
> Back Off! I just backed up ener.edr to ./#ener.edr.3#
> starting mdrun 'Protein in water'
> 5000 steps,     10.0 ps.
>
>
> Back Off! I just backed up peptido_md.trr to ./#peptido_md.trr.3#
> step 90, remaining runtime:   269 s
> Back Off! I just backed up step100.pdb to ./#step100.pdb.1#
> Wrote pdb files with previous and current coordinates
> step 100, remaining runtime:   291 s
> Back Off! I just backed up step103.pdb to ./#step103.pdb.1#
>
> Back Off! I just backed up step104.pdb to ./#step104.pdb.2#
> Wrote pdb files with previous and current coordinates
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
>
>
>
>
> Osmany Guirola Cruz wrote:
>
>
>
> Ok, thanks Xavier, but i read in some papers that they modify  bond 
> angles and bond
> length,  for give more "movility" to the system and guarantee a great 
> SA. How could ido this with
> gromacs
>
>
> Xavier Periole wrote:
>
> What time is necesary for cooling a sistem? everybody say SLOWLY .
>
>
>
>
> Depends the type of system, its size, the purpose of the simulated
> annealing.
> But yes the slowest the better. At the origin the simulated annealing 
> was
> coupled to Monte Carlo simulation and in THEORY if you decrease the
> temperature by steps infinitey small you get to the global minimum. 
> Check
> in a book or some papers using simulated annealing.
>
> XAvier
>
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>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel
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