Dear Justin, Thank you, that's the first help I have had. In any case, I will look at the .mdp file , as I was using a test structure I already ran through an MD. I had gone from 4.0.7 to 4.5.1 to 4.5.3, the first two ran MD's. Now I am rolling back too 4.0.7, but have not recieved complaints from the software in preperation other then rlistlong not found, etc...and the posted errors
> Message: 6 > Date: Tue, 21 Dec 2010 15:25:06 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Re:Crash error > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4d110d22.5040...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > lloyd riggs wrote: > > Dear All, > > > > I had posted part of the error below. I still have not the problem > solved, everything from gromacs runs, including short energy minimizations, > but > if I run an MD I get the log ending; > > > > Started mdrun on node 0 Thu Dec 9 16:56:10 2010 > > > > Step Time Lambda > > 0 0.00000 0.00000 > > > > Grid: 10 x 10 x 10 cells > > Long Range LJ corr.: <C6> 2.3566e-03 > > Long Range LJ corr.: Epot -59.767, Pres: -0.198483, Vir: 29.8835 > > Energies (kJ/mol) > > G96Bond G96Angle Proper Dih. Improper Dih. > LJ-14 > > 1.19873e+04 5.04804e+03 5.15110e+03 1.67253e+03 > 1.49605e+00 > > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) RF > excl. > > 1.15200e+05 2.87676e+09 -5.97670e+01 -1.24355e+05 > -7.20279e+04 > > Potential Kinetic En. Total Energy Temperature Pressure > (bar) > > 2.87670e+09 4.35260e+17 4.35260e+17 4.13944e+15 > 9.63648e+14 > > > > ________________________ > > > > and the error log; > > > > > > Reading file > /home/ubelix/l_insel_ria/l_watkins/gormacswork/Test4gromacs/md1.tpr, VERSION > 4.0.7 (double precision) > > starting mdrun 'Protein' > > 100000 steps, 200.0 ps. > > [cnode33:13647] *** Process received signal *** > > [cnode33:13647] Signal: Segmentation fault (11) > > [cnode33:13647] Signal code: Address not mapped (1) > > [cnode33:13647] Failing at address: 0x237fa90 > > [cnode33:13647] [ 0] /lib/libpthread.so.0(+0xf010) [0x2b6e69c97010] > > [cnode33:13647] [ 1] /usr/lib/libgmx_mpi_d.so.5(+0x115564) > [0x2b6e69491564] > > [cnode33:13647] *** End of error message *** > > > > I am trying still to find out how to fix it, and if it is a problem with > the two files listed, or they are just the last ones called. > > > > Your system is blowing up. Since it's happening at step 0, it's likely > due to > some physically unreasonable geometry. Note that temperature, pressure, > etc are > all astronomically high. > > Whatever your previous preparation steps (minimization, equilibration), > they > were likely insufficient. Otherwise, your .mdp file settings are creating > the > problem. > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > -Justin > > > Hollidays > > > > Stephan Watkins > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern E-Mail & mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail -- 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
