From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Aug 31 2015 - 08:30:48 CDT
Dear Monika,
This may be a silly question, but did you turn on the tip4p water model in your config file?
Best,
Peter
> On Aug 31, 2015, at 6:42 AM, Monika Madhavi <monikamadhavi_at_gmail.com> wrote:
>
> 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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