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

Kenji Mochizuki kmochi at ims.ac.jp
Wed Mar 20 02:58:29 CET 2013


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
===============

==== .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





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