Atoms moving too fast; simulation has become unstable

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Aug 31 2015 - 05:42:48 CDT

Dear all,

I want to simulate water dynamics using TIP4P water model. My simulation
box contains only water. For this I created my own parameter and topology
files based on data available on some references. But when I try to
simulate, the minimization goes OK but when it starts to equilibrate, it
says "Atoms moving too fast; simulation has become unstable" and stops.
When I examined the last frame, it seems that the structure is distorted. I
think it may be due to an error in topology and parameters. Could you
please suggest what is the correct way of writing parameters and topology
files for namd simulations?

The used files are as follows.

!parameter file for TIP4P water
!
BONDS
!atom type Kb b0
HW HW 0.000 1.5139
OW HW 450.000 0.9572
OW OM 0.000 0.1577
ANGLES
!atom type Ktheta Theta Kub S0
HW OW HW 55.00 104.52
HW OW OM 50.00 52.26
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
OW 0.000000 -0.155300 1.576825
HW 0.000000 0.000000 0.000000
OM 0.000000 0.000000 0.00000
END

!topology for TIP4P water
!
MASS 300 HW 1.00800
MASS 301 OW 15.99940
MASS 302 OM 0.00000

RESI TP4P 0.000
GROUP
ATOM OW OW 0.0000
ATOM HW1 HW 0.5200
ATOM HW2 HW 0.5200
ATOM OM OM -1.0400
BOND OW HW1 OW HW2 OW OM
!HW1 HW2 !this bond needed for SHAKE but not in NAMD
ANGLE HW1 OW HW2 HW1 OW OM HW2 OW OM

IC HW1 OW OM HW2 0.9572 52.26 180.00 119.50 0.8697
IC HW2 HW1 OW OM 1.5139 37.74 0.00 52.26 0.1577
ACCEPTOR OM
PATCHING FIRS NONE LAST NONE
END

Thank you.
Monika

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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