[gmx-users] Normal Mode Analysis

[Justin A. Lemkul]

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

-- 
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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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