[gmx-users] Normal Mode Analysis

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> 
> I've forced with the problem that I could not prorerly minimized my 
> system in the NMA conditions. Even in STEEP minimizaation I could not 
> obtain Epot value lower than +3.00 with that parametries ( I've used 
> KALP peptide as a test input )
> 

The Epot value is less significant than Fmax (which is what is set in the .mdp 
file, anyway).  What Fmax do you achieve?  Real copied and pasted output would 
be useful.

> ; Parameters describing what to do, when to stop and what to save
> integrator    = steep       
> emtol        = 1      ; Stop minimization when the maximum force < 1.0 
> kJ/mol/nm
> emstep      = 0.01      ; Energy step size
> nsteps        = 5000000          ; Maximum number of (minimization) 
> steps to perform
> 
> 
> 
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist        = 1        ; Frequency to update the neighbor list and 
> long range forces
> ns_type        = grid        ; Method to determine neighbor list 
> (simple, grid)
> rlist        = 1.2        ; Cut-off for making neighbor list (short 
> range forces)
> coulombtype    = Shift   
> rcoulomb        = 1.0
> rcoulomb_switch    = 0.0
> vdwtype         = Shift
> rvdw        = 1.0
> rvdw_switch     = 0.0   
> 
> Than I've tried to futher minimized this structure via  l-bfgs algorithm by
> 
> integrator    = l-bfgs
> dt                  =  0.01
> emtol        = 0.001     ;
> emstep      = 0.1      ; Energy step size
> nsteps        = 50000000          ; Maximum number of (minimization) 
> steps to perform
> 
> but Epot was still big.
> 
> What I've done wrong ?

Are you using single- or double-precision?

-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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