[gmx-users] Normal mode analysis error

[Justin Lemkul]

On 3/17/15 8:16 AM, rahul dhakne wrote:
> Dear all,
>
>
> I am trying to perform the Normal Mode Analysis protein in water.
> Here is the .mdp file I am using:
>
>
> integrator          = nm                    ; time step
> nsteps              =  100000                  ; number of steps
> nstlist             =  10                        ; update pairlist
> ns_type             =  grid                     ; pairlist methodi
> coulombtype         =  PME
> nstxtcout           =  1.0
> cutoff-scheme       = Verlet
> rcoulomb            =  1.0
> rvdw                =  1.0
> ewald_rtol          =  1.0
> rlist               =  1.0                      ; cut-off for ns
> constraints         = none
> define              = -DWHATEVER
>
>
>
> And I get the error message:
>
> Fatal error:
> Constraints present with Normal Mode Analysis, this combination is not
> supported.
>

It's probably from the water, which have SETTLE constraints.  In this case you 
need -DFLEXIBLE or however the water topology might disable SETTLE.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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