On 3/19/13 9:58 PM, Kenji Mochizuki wrote:
> Dear gromacs users
>
> 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
> ===
>
These messages are coming from your cluster's management system. You should
consult your sysadmins; this is not a Gromacs problem.
-Justin
> .top file
> [ defaults ]
> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
>1 2 no 1.0 1.0
> [atomtypes]
> ;name mass charge ptypesigmaepsilon
> IW 0 0.000 D 0.0 0.0
> OWT4 15.99940 0.000 A 0.31668 0.88211
> HW 1.00800 0.000 A 0.0E+00 0.0E+00
> [moleculetype]
> ; name nrexcl
> SOL 1
> [atoms]
> ; nr type resnr residu atom cgnr charge
> 1 OWT4 1 water OW 1 0 15.994
> 2 HW 1 water HW1 1 0.58971.008
> 3 HW 1 water HW2 1 0.58971.008
> 4 IW 1 water MW 1-1.17940.0
> [constraints]
> ;i j funct doh dhh
> 1 2 1 0.09572
> 1 3 1 0.09572
> 2 3 1 0.15139
> [exclusions]
> 1 2 3 4
> 2 1 3 4
> 3 1 2 4
> 4 1 2 3
> [dummies3]
> ; Dummy fromfunct a b
> 4 1 2 3 1 0.13458 0.13458
> [system]
> water TIP4P/Ice
> [molecules]
> SOL 433
> =
>
> Kenji
>
>
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
