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

[Michael Shirts]

And with this change, single is running fine as well.

This was a known issue, but was only documented in the expanded.mdp
files, which was an oversight.  After this, I switched so the default
is less likely to cause problems.  Because of some theory improvements
developed in the group in free energy calculation pathways, the
sc-r-power=48 pathway will now be phased out anyway by 5.1.

On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts <mrshirts at gmail.com> wrote:
> 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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