From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Sep 17 2015 - 04:42:40 CDT
Thanks for your time. Farzad by the model, are you referring to the pdb or
topology. I think my pdb is fine but I am not sure about the topology
whether I need to define some lone pairs. I tried with smaller time steps.
Still getting the same error.
Peter, I tried with turning on tip4p water model in config file and
without. Both failed. Is there a specific way that I should define the lone
On Mon, Aug 31, 2015 at 7:00 PM, Peter Freddolino <petefred_at_umich.edu>
> Dear Monika,
> This may be a silly question, but did you turn on the tip4p water model in
> your config file?
> > On Aug 31, 2015, at 6:42 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
> > 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
> > !
> > 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.
-- W.A.Monika Madhavi Lecturer (Probation), Department of Physics, University of Colombo.
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