[gmx-users] minimzation problem with a heterogeneous system

[Justin A. Lemkul]

Quoting Payman Pirzadeh <ppirzade at ucalgary.ca>:

> Dear Mark,
> I think I know the problem! I have simulated homogeneous systems (liquid
> water) without any problems. Problem is with the order of particles in the
> PDB or gro file which I use as my input. As the order of oxygen changes in
> the input, when I 'settle' the oxygen, then the corresponding Hs are not
> after my oxygen. So, settle takes sth else for constraining the system. Now,

Didn't grompp warn you that atom names did not match the topology?

> I need a smart advice on how to convert the order of particles in PDB or gro
> file in way that it matches the OHH format, not sth else.
>

Probably could be done with a simple Perl script to sort the atoms based on
name, for each residue number.

-Justin

> Payman
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Mark Abraham
> Sent: Thursday, July 16, 2009 8:40 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] minimzation problem with a heterogeneous system
>
> Payman Pirzadeh wrote:
> > 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.
>
> All we can say is the something is broken with your model or initial
> configuration. Simplify it into small, homogeneous systems until you can
> diagnose the source of the problem.
>
> Mark
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================