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 ======================================== -- gmx-users mailing list gmx-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
