On 11/15/12 9:03 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <[email protected]> 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.
-Justin
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
--
========================================
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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