From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Aug 31 2015 - 06:29:30 CDT
Hello Monika
After running the simulation at constant pressure for say 50 ps (1 fs
steps). You can run the simulation under constant NVT conditions. Try this
after going through the steps suggested by Farzad.
Regards
Sourav
On Mon, Aug 31, 2015 at 4:47 PM, farzad kiani <
farzad_kiani1364_at_remove_yahoo.com> wrote:
> Dear Monika,
>
> If you have chosen topology file from NAMD's data base, your guess could
> be a wrong guess.
> As I know there could be three ways to alleviate the problem.
> Firstly, may be you have created a bad model. If you are certain about the
> model, check periodic box dimensions, temperature and pressure in the
> config file. Sometimes you can used a little bigger periodic box (1 to 3
> Angstrom bigger than that is calculated by VMD). Finally, if all above
> statuses are correct, apply smaller time steps to initialization the
> model. After enough time steps, stop the run and take bigger time steps. I
> think your model need to initialize smoothly.
>
> Kind regards
> Farzad Kiani
>
>
>
> On Monday, August 31, 2015 3:15 PM, 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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