[gmx-users] Cannot minimiza - vdwradii.dat ???
s.neumann08 at gmail.com
Thu Nov 15 15:03:32 CET 2012
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
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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