[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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