[gmx-users] Energy minimization
andreab at physiol.unizh.ch
Mon Jan 10 15:36:56 CET 2005
I'm very new in the use of Gromacs 3.2 and I would like to ask people
with more experience than me about the energy minimization procedure.
I'm trying to minimize the energy of a protein I obtained by homology
modelling (it's about 500 aa) following a paper where the authors did a
work similar to the one I'm doing now. My problem is simple:
in this paper authors say : "Electrostatic forces were calculated with
the particle-mesh Ewald algorithm. Initial energy minimization was done
with the steep descent algorithm (1000 steps) followed by conjugate
gradient to a maximum force of 0.1 Kj mol^-1 nm^-1 ." do they mean that
in the same em.mdp script they used both s.d and c.g one after the
other? I all the tutorials I found the energy minimization was done by
using either one or the other algorithm, or using the nstcgsteep option
with c.g as main algorithm, so how can you use (if its possible) one
algorithm and then the other in the same em.mdp script?
Minimizing the protein energy using Gromacs with single precision, no
constraints, cg and nstcgsteep gives an Fmax of 50 Kj mol^-1 nm^-1 , if
I go below this value the system converge to machine precison but not to
the requested Fmax (lets say 10 Kj mol^-1 nm^-1 ).
My goal is to improve the reached Fmax up to the paper's level, if it's
possible, and then run a full molecular dinamic simulation in water.
Thank you for your attention and help
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