James Starlight wrote:
Mark, hello!
I think that there is some error durins saving of my minimization data
As the result of the minimization I've obtained
(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy = 2.08789280994511e+03
Maximum force = 3.01715687185776e-04 on atom 58
Norm of force = 3.09301310600005e-05
So the Fmax is sufficient low
But when I've load this data for NMA I've obtained
(2)
Maximum force: 8.41270e+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.
So the Fmax is indeed very big for NMA but why it's not the same as in
the (1)?
This is my script for NMA wich indicate that I've load to NMA suitable data
# Steep
grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr
mdrun_d -v -deffnm minimizedS
# Grad
grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o
minimizedGRAD.tpr
mdrun_d -v -deffnm minimizedGRAD
# NMA
grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr
mdrun_d -v -deffnm fornma -mtx nm.mtx
Where is the error?
You're using the unminimized coordinates as input into NMA. The file
"minimizedGRAD.tpr" contains the configuration before doing L-BFGS minimization,
so it is not sufficiently minimized.
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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