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 = 10 ; 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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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