[gmx-users] minimzation problem with a heterogeneous system

[Payman Pirzadeh]

Hello,
I have a configuration in which half of the box is liquid water and the
other half is ice. This configuration is the output of another simulation in
which the mentioned config worked (and still works fine). But when I start
minimizing it (I started minimization since my first round of MD run crashed
due to messages indicative of clashes). But minimation ends with the
following message:

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e-06
   Number of steps    =       500000
Step=    1, Dmax= 1.0e-01 nm, Epot=  6.09464e+11 Fmax= 1.31718e+14, atom=
2938
Step=    2, Dmax= 1.2e-01 nm, Epot=  1.15027e+09 Fmax= 2.00242e+11, atom=
2576
Step=    3, Dmax= 1.4e-01 nm, Epot=  1.56529e+08 Fmax= 2.20702e+09, atom=
11062

t = 0.004 ps: Water molecule starting at atom 16078 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step=    4, Dmax= 1.7e-01 nm, Epot=  2.11002e+10 Fmax= 5.75671e+13, atom=
14986
t = 0.005 ps: Water molecule starting at atom 14902 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step=    5, Dmax= 8.6e-02 nm, Epot=  1.22915e+07 Fmax= 4.57843e+07, atom=
6280

t = 0.006 ps: Water molecule starting at atom 15952 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step=    7, Dmax= 5.2e-02 nm, Epot=  5.50887e+06 Fmax= 1.19611e+08, atom=
7348
Step=    8, Dmax= 6.2e-02 nm, Epot=  4.29974e+06 Fmax= 1.39548e+07, atom=
12066
Step=    9, Dmax= 7.5e-02 nm, Epot=  1.93270e+06 Fmax= 2.81542e+07, atom=
7204

t = 0.010 ps: Water molecule starting at atom 7300 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step=   26, Dmax= 1.4e-06 nm, Epot=  2.53306e+06 Fmax= 8.74996e+06, atom=
15953
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1e-06

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 27 steps,
but did not reach the requested Fmax < 1e-06.
Potential Energy  =  1.9327006e+06
Maximum force     =  2.8154184e+07 on atom 7204
Norm of force     =  4.1820662e+05

I checked the output .pdb files, and they show box is cracking from the
position of the ice-water interface! Also, the ice part looks like a
complete mess! (like it's not going to be ice anymore). I checked the .itp
file to make sure are the variables are correct. Nothing looked wrong to me.
I checked the mailing list about minimization. Just remember this water
model is not flexible. 
Regards,

Payman


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: July 16, 2009 12:39 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water

Payman Pirzadeh wrote:
> You were right! The dimensions of the box are zero in the .gro file.
Should
> I change them to the values I have?

Set them using editconf

Mark
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