[gmx-users] Re: memory excess error of Tip4p/Ice model

[Dr. Vitaly Chaban]

> I have performed MD simulation using Tip4p/ice model, which is copied from
> [http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model]
>
> The MD actually works and the output structure looks fine.
> However, after 11ns run, the run was suddenly stopped and I got the following error message.
>
> In case of Tip4p, in which .top file contains
> #include "ffoplsaa.itp"
> #include "tip4p.itp"
> the MD run works well and never stop, although I used the same .mdp and .gro file.
>
> The difference of two MD runs is just .top file,
> so I suspect .top file for tip4p/ice has something wrong.
>
> Could you please give me advise to fix it ?
>
> Regards
>
> ==== Error ====
> tput: No value for $TERM and no -T specified
> =>> PBS: job killed: mem 33310024kb exceeded limit 32505856kb
> ===============


Gromacs cannot use 33GB of memory, unless you simulate something monstrous.

At the same time, topology file, either correct or incorrect, cannot
engender  memory errors.

To recapitulate, this is a strange error originating within your
particular computational node,

Dr. Vitaly Chaban