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

[Justin Lemkul]

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 ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>    1             2               no              1.0     1.0
> [atomtypes]
> ;name     mass      charge   ptype    sigma        epsilon
> 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   0.00000E+00   0.00000E+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     0.5897    1.008
> 3     HW   1     water  HW2  1     0.5897    1.008
> 4     IW   1     water  MW   1    -1.1794    0.0
> [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 from                    funct   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

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