[gmx-users] Assertion failed for the REMD tutorial

[Alessandra Villa]

Hi,

On Tue, Jan 21, 2020 at 9:55 PM ZHANG Cheng <272699575 at qq.com> wrote:

> I am trying to follow the REMD from Mark Abraham at
>
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
>
>
>
The tutorial was meant for the GROMACS version 4.6.3. As I can see from the
md.log file, you are using version 2019.3.
As the md.log shows, you have a lot of obsolete mdp entry. Better to update
the mdp entries.
(see
http://manual.gromacs.org/2019-current/user-guide/mdp-options.html#mdp-general
)




> At Stage 2, when I run the grompp command
> (for dir in sim[0123]; do cd $dir; gmx grompp -f sim -c confout -t
> equil-state; cd ..; done)
>
>
> I got error message:
>
>
> Program:&nbsp; &nbsp; &nbsp;gmx grompp, version 2019.3
> Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
> Function:&nbsp; &nbsp; lambda []()-&gt;auto::operator()()-&gt;auto
> Assertion failed:
> Condition: list != nullptr || (v != nullptr &amp;&amp; vector == nullptr)
> || (v == nullptr &amp;&amp; vector != nullptr)
> Without list, we should have exactly one of v and vector != NULL
>
>
>
  md.log reports a problem with the checkpoint file that you provide to
grompp with the option -t (maybe the file was generated with an older
GROMACS version? or for a different system?)

Best regards
Alessandra


>
> The whole log is uploaded at
>
> https://github.com/lanselibai/gromacs-20200121/blob/master/Assertion%20failed.log
>
>
> Can I ask how to solve this? Thank you!
> --
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