[gmx-users] About Pulling code in Gromacs 5.0.2

[hang yin]

Thank you Alex.

So did you mean the pulling with the absolute reference is nothing related
to the error?
My pulling rate is 0.01nm/ns, slow enough I think. I am going to double
check if the system is stable without pulling.

Hang

2015-06-10 15:31 GMT+08:00 Alex <nedomacho at gmail.com>:

> The artifacts warning is general (mentioned in the manual) and has nothing
> to do with your
> system (aside from your mdp), everyone using absolute reference frame
> gets this warning.
>
> That said, the error you're getting is actually descriptive. So:
>
> 1. Check if the system is stable and happy without pulling.
> 2. Make sure the pulling rate is compatible with your nstlist setting.
> If the neighbor list update rate can't keep up with your pulling rate,
> that's a problem. High pulling rates in thermostatted systems are also
> generally problematic from the physical standpoint. Severely
> problematic. Steered MD is to be carefully designed.
> 3. Make sure your boundaries are taken care of properly, in case your
> pulled object meets the wall.
>
> Alex
>
>
>
> hy> Hello all,
>
> hy> Recently, I preformed a SMD, pulling a nano diamond across the
> membrane. I
> hy> found that pull_geometry position in the Gromacs 4.6.5 (suggested in
> the
> hy> tips of the US tutorial by Justin.A ) was replaced by pulling with
> absolute
> hy> reference point in Gromacs 5.0.2. After defined pulling parameters
> hy> according to the manual, Gromacs gave me a warning that "This will
> lead to
> hy> artifacts". I really want to know what did it mean, so I ignored it by
> hy> using maxwarn 1 and saw what would happen. Finally I got a segment
> fault
> hy> that a bonded atom moved away, out of the cut-off distance.
>
> hy> Can you give me some advises? How can I treat the pulling correctly for
> hy> this penetrating process and why does the absolute reference lead to
> hy> artifacts.
>
> hy> Many thanks!
>
> hy> Hang
>
>
>
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