[gmx-users] Cannot minimiza - vdwradii.dat ???
jalemkul at vt.edu
Thu Nov 15 15:30:11 CET 2012
On 11/15/12 9:03 AM, Steven Neumann wrote:
> On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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.
> This is Fe(2+) - from trjactory it can be observed that it collides
> with negatively charged oxygen from my other small molecule. Are you
> sure that vdwradii.dat wont solve it while placing molecules using
> genbox and then solvating. The vdw radius of Fe(2+) is 2 A. Would you
> suggest something?
Try it and see. If genbox doesn't find a radius, it uses a default value, which
is specified with -vdwd on the command line, so modifications to vdwradii.dat
are not strictly necessary, but a more explicit command might be.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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