[gmx-users] minimization problem (Martini simulation)

[Justin A. Lemkul]

politr at 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

-- 
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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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