my peptide have 11 amino acids and it is cyclic
Post by Kay GottschalkAt 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?
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[ 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[ 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[ 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[ 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[ 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]
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
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
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