Naba wrote:
Dear Mark,
> I am using Gromacs 4.0.5. I have invested a considerable amount of
time in
> searching literature and mailing lists to perform at least a
successful NM.
> I have posted this problem in the mailing lists but I need some quick and
> confirmed reply. So I mailed you directly, please don't mind. If
anything is
> missing in illustrating my problem kindly let me know I will try to
provide
> the missing information.
Please leave correspondence on the list. I'm not going to reply any
faster to a personal email.
I encountered a similar problem in running NM,
.. similar to what? We don't necessarily remember your context. Please
quote relevant previous emails as suitable :-)
and even if i minimized the
whole protein in vacuum 1st with steepest descent, 2nd conjugate gradient,
and finally l-bfgs, for 5000, 1000, and 100000 steps, respectively to
converge the same tolerance 0.001. But only l-bfgs converges to Fmax. I
have tried several times to analyze the results of NM but when I saw the
eigenval.xvg, the values are in the order of -0.2 to -0.8. So I left the
hope and trying to restart with new parameters.
l-bfgs gives the following output:
Step 50485, Epot=-1.532957e+04, Fnorm=3.960e-04, Fmax=3.798e-03 (atom 4664)
Step 50486, Epot=-1.532957e+04, Fnorm=1.919e-04, Fmax=1.353e-03 (atom 4664)
Step 50487, Epot=-1.532957e+04, Fnorm=1.574e-04, Fmax=8.890e-04 (atom 3370)
writing lowest energy coordinates.
Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 50487 steps
Potential Energy = -1.53295718433487e+04
Maximum force = 8.88978297012589e-04 on atom 3370
Norm of force = 1.57441192362912e-04
I included .trr files in each and every energy minimization. But still when
running NM mdrun gives the following message:
Using compressed symmetric sparse Hessian format.
Allocating Hessian memory...
starting normal mode calculation 'Protein'
5143 steps.
Maximum force: 9.75763e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.
I could not get what is wrong after going through some considerable extent
of literature. It's really panic to have useless results since the Hessian
comprises negative eigenvalues. My maximum force at the end of l-bfgs has
not been taken my NM mdrun. Why??
That will depend on which structure you take for the second
minimization. You probably need to provide the full-precision structure
from the previous .trr file to grompp, not a .gro or .pdb file.
As Mark pointed out to perturb the system in the direction of some
eigenvector, I also feel that my system may be in some non-minimum
stationary point. And I would like ask how to do that?
Find the atoms with the largest motions along the corresponding
eigenvector and perturb their coordinates correspondingly by hand using
a text editor on the structure file. This is a standard quantum
chemistry technique from the days before intrinsic reaction coordinate
following methods.
I have tested the same procedure to calculate normal modes with another
protein with 298 residues. But same problem occurred again and again.
However, the thread of this discussion ended with the solution to this
problem which is to ignore gro files as they do not have precision in
coordinates. But without a gro file how does one run grompp I could not get.
Read grompp -h. There's a flag that accepts a trajectory file as input.
You will also need to supply a full coordinate file for atom names and
such, but importantly, grompp takes the final trajectory configuration
as the starting point for the next run.
Mark
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