pol...@fh.huji.ac.il wrote:
Dear Gromacs users and developers,
I forgot to note that I'm talking about a Martini simulation.
I'm trying to set up simulation. I have a big simulation of something
like half million CG atoms. The problem is that I have a minimization
problem. I'm getting the following error:
Converged to machine precision,
but not to the requested precision Fmax < 10
This is not really an error:
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
The success of any subsequent MD depends on the magnitude of the maximum force
the EM procedure achieved. Minimizing to such a low force is very difficult and
may not be possible for all systems.
I tried to use a bigger emtol(emtol=20) and it still didn't
converge.However I still run the MD with dt = 0.03 and nstxout = 1.
after something like 100 steps the system blow up.
Perhaps your EM wasn't sufficient, but based on the information you've posted,
it's hard to draw any real conclusion about that.
I will appreciate any help with this issue.
Many thanks in advance.
P.S May it help if I minimize a smaller system and replicate it after
that. How exactly can I do replication?
It may or may not help, but I don't think it likely. You can always try it and
see. Certainly minimizing a smaller system will give you a faster result. You
can replicate any unit cell in any dimension using genconf -nbox.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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