On Jan 10, 2005, at 4:36 PM, Andrea Bacconi wrote:
Hallo everybody,
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?
If they work with GROMACS they used two stages process, with two
files.
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?
Use the output from the steep run as input to the CG run.
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.
This happens, do full MD with this structure, do not forget to
solvate the protein properly (adding water;EM ; MD where the protein
it PR ; full MD).
Thank you for your attention and help
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