From: farzad kiani (farzad_kiani1364_at_yahoo.com)
Date: Mon Aug 31 2015 - 06:17:38 CDT
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 regardsFarzad 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 MadhaviLecturer (Probation),Department of Physics,University of Colombo.
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