On 3/15/17 1:19 PM, Dayhoff, Guy wrote:
I have a drude system that I have minimized, and equilibrated through nvt
and npt ensembles using position restraints (all with scf). As I perform the
production runs i’m facing random crashes that seem to be related to EM
did not converge messages. This has happened anywhere from tens of
thousands of steps in, to millions of steps in. Below is an example and
the mdp options for the run.
Please contact me off-list about this. These are not officially supported
features and there are possibly bugs but I will need better descriptions of what
you're doing and all your input files.
-Justin
My Best,
Guy Dayhoff
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
step 393698: EM did not converge in 20 iterations, RMS force 15.668
step 393699: EM did not converge in 20 iterations, RMS force 88.569
step 393700: EM did not converge in 20 iterations, RMS force 341.002
step 393701: EM did not converge in 20 iterations, RMS force 680.888
step 393702: EM did not converge in 20 iterations, RMS force 1147.229
step 393703: EM did not converge in 20 iterations, RMS force 1077.486
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
MDP options:
; RUN CONTROL
integrator = md
nsteps = 5000 ;50ns
dt = 0.001
; OUTPUT CONTROL
nstxout = 0
nstvout = 1 ;every 10ps for now
nstfout = 1
nstlog = 1
nstenergy= 1
nstcalcenergy= 1
nstxout-compressed = 1
compressed-x-grps= System
; NEIGHBOR SEARCHING
cutoff-scheme= verlet
nstlist = 10
ns-type = Grid
pbc = xyz
rlist= 1.2
; BONDS
constraints = h-bonds
continuation = yes
; ELECTROSTATICS AND VdW
coulombtype = PME
rcoulomb = 1.2
vdwtype = cutoff
vdw-modifier = potential-switch
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
; EWALD
pme_order= 4
fourierspacing = 0.16
; TEMPERATURE COUPLING
Tcoupl = Nose-Hoover
tc-grps = Water non-Water
tau_t= 10.0 10.0
ref_t= 300 300
nh-chain-length = 1
; VELOCITY GENERATION
gen-vel = no
; PRESSURE COUPLING
Pcoupl = Parrinello-Rahman
Pcoupltype = semiisotropic
tau_p= 50.0
compressibility = 4.5e-5 4.5e-5
ref_p= 0.0 3.0
; DRUDE POLARIZATION
drude = yes
drude-mode = SCF
drude-hyper = yes
drude-khyp = 16736000.0
drude-r = 0.02
drude-pow = 4
--
==
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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