Re: Atoms moving too fast; simulation has become unstable

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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