Hi,
On Tue, Jan 21, 2020 at 9:55 PM ZHANG Cheng <272699...@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: gmx grompp, version 2019.3
> Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
> Function: lambda []()-auto::operator()()-auto
> Assertion failed:
> Condition: list != nullptr || (v != nullptr vector == nullptr)
> || (v == nullptr 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!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
