[gmx-users] Cannot minimiza - vdwradii.dat ???

[Justin Lemkul]

On 11/15/12 8:41 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I am trying to run simulations of protein and FE(2+) atoms. I placed
> them randomly around the protein, solvated the system and tried to
> minimize. After grompp, I tried mdrun:
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
> 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)
>
> Steepest Descents converged to machine precision in 62 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -7.2573600e+05
> Maximum force     =  5.7863950e+05 on atom 756
> Norm of force     =  3.5862925e+03
>
> I tried different stepsizes, constarint = none etc but never converged
> to requested Fmax < 1000
>
> When I try NVT:
>
> Fatal error:
> 2 particles communicated to PME node 0 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
>
> So the problem is with minimization.
>
> My question: Can it be the problem of not specified vdwradius of my
> FE(2+) in vdwradii.dat ? I mean, can ater molecules overlap with
> Ferrous and thus minimization does not converge?
>

The problem is unrelated to vdwradii.dat, which is only used for neighbor 
searching with genbox.  mdrun tells you there is a problem with atom 756.  What 
is it?  What is it interacting with?  That's how you trace the problem.

-Justin

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

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