[gmx-users] NMA Fatal Error

[Justin Lemkul]

On 11/16/12 3:43 PM, Yao Yao wrote:
> Hi Gmxers,
>
> I am doing a protein NMA with the mdp file like,
>
> ===========================================
>
>
> define          = -DEFLEXIBLE
> constraints     = none
> integrator      = nm ;
> emtol           = 0.00001
> emstep          = 0.1
> nsteps          = 4000  ; Maximum number of (minimization) steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> nstlist         = 0 ; Frequency to update the neighbor list and long range forces
> ns_type         = simple        ; Method to determine neighbor list (simple, grid)
> ;vdwtype         = switch
> vdwtype         = cut-off
> rlist           = 0.0   ; Cut-off for making neighbor list (short range forces)
> ;coulombtype    = PME-switch    ; Treatment of long range electrostatic interactions
> coulombtype     = cut-off
> ;rcoulomb       = 1.2   ; Short-range electrostatic cut-off
> rcoulomb        = 0.0
> ;rvdw           = 1.2   ; Short-range Van der Waals cut-off
> rvdw            = 0.0
> pme_order       = 4
> fourierspacing  = 0.12
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> optimize_fft    = yes
> pbc             = no
> =====================================================
>   However, it shows
>
>
> "Fatal error:
> Constraints present with Normal Mode Analysis, this combination is not supported"
>
> Since I put "Constaints" none, I really do not get it. Can someone help me?
>

The problem is a typo.  You've set "-DEFLEXIBLE" instead of "-DFLEXIBLE" so 
rather than having flexible water as intended, you've got rigid water via the 
SETTLE algorithm, and constraints are still present.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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