[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

[Michael Shirts]

I thought I had just managed to solve the issue :)

If you look at the soft core parameters, there are two types listed --
one with sc-r-power = 48, and one with sc-r-power = 6.  The sc-r-power
are more stable with single precision calculations.

I have changed the files on the website to make the single precision
ones the default.  Expanded.mdp warned about the issues with
precision, but left the sc-r-power in place; the Ethanol.mdp did not
warn about the potential issue.  Now both include the more efficient
path commented out.

NOTE that this means the exact numbers of the tutorials are not quite
right anymore; the process is unchanged, as is the final answer, but
the intermediate dG's will be slightly different.

However, I need to redo them anyway to make them easier in the next
1-2 weeks, so I will update them then.

If it still fails with double, that's a different issue -- because I'm
running them fine with double.





On Thu, Sep 26, 2013 at 6:32 PM, Christopher Neale
<chris.neale at mail.utoronto.ca> wrote:
> My mistake .... I still get a segfault even when using double precision. (EM doesn't help, nor does switching to Berendsen pressure coupling).
>
> Note that I can stop the segfault when running at init-lambda-state = 0 if I set:
>
> couple-lambda0           = none
> couple-lambda1           = none
>
> instead of
>
> couple-lambda0           = vdw-q
> couple-lambda1           = none
>
> This looks like http://bugzilla.gromacs.org/issues/1306
>
> Thank you,
> Chris.
>
> -- original message --
>
> Thank you Mark.
>
> I actually found that it crashed wihout the -multi part (no hamiltonian exchange).
> The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg
>
> If I use the double precision version, there is no segfault. That's a working solution, but it is worrysome.
>
> Thank you,
> Chris.
>
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