[gmx-users] Simulated annealing 10000K

[Osmany Guirola Cruz]

my peptide have 11 amino acids and it is cyclic

Kay Gottschalk wrote:

> 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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>
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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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