Dear Ainun. It looks like your system is exploding. Check the input coordinates. Cheers Cesar El 03/10/2014 01:10, "AINUN NIZAR M" <0810710...@mail.ub.ac.id> escribió:
> Dear users, > > I conduct folding simulation, this is my trial project before I conduct my > own one. I simulate small protein, 1CRN. The aim is that i can simulate > folding from primary protein structure to a fully-folded 3rd structure. To > create primary protein structure, I created 1CRN.pdb based on fasta > sequence using swisspdbviewer, then i use it in gromacs. > > After some preparation, I had succesfully minimized the protein using steep > depest minimization. The I did nvt equilibration. Warning and Error was > occured: > > > > > > > > > > > > > > *WARNING: Listed nonbonded interaction between particles 206 and 207at > distance 23490.299 which is larger than the table limit 151.000 nm.This is > likely either a 1,4 interaction, or a listed interaction insidea smaller > molecule you are decoupling during a free energy calculation.Since > interactions at distances beyond the table cannot be computed,they are > skipped until they are inside the table limit again. You willonly see this > message once, even if it occurs for several interactions.IMPORTANT: This > should not happen in a stable simulation, so there isprobably something > wrong with your system. Only change the table-extensiondistance in the mdp > file if you are really sure that is the reason.* > > warning disnt appear anymore after i increased the value of table-extension > to very high. however there still error message in nvt equilibration so > that i cant continoue to the next step. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *GROMACS: gmx mdrun, VERSION 5.0Executable: > /usr/local/gromacs/bin//gmxLibrary dir: > /usr/local/gromacs/share/gromacs/topCommand line: mdrun -nt 2 -deffnm > nvtBack Off! I just backed up nvt.log to ./#nvt.log.9#Reading file nvt.tpr, > VERSION 5.0 (single precision)Changing nstlist from 10 to 40, rlist from 1 > to 1Using 1 MPI threadUsing 2 OpenMP threads Back Off! I just backed up > nvt.trr to ./#nvt.trr.9#Back Off! I just backed up nvt.edr to > ./#nvt.edr.9#Back Off! I just backed up nvt.xvg to ./#nvt.xvg.9#starting > mdrun 'Protein in water'5000 steps, 10.0 ps.Step 0, time 0 (ps) LINCS > WARNINGrelative constraint deviation after LINCS:rms 125.551300, max > 1177.774780 (between atoms 268 and 269)bonds that rotated more than 30 > degrees: atom 1 atom 2 angle previous, current, constraint length > 118 119 90.0 0.1090 0.1947 0.1090 264 265 90.0 > 0.1090 0.1967 0.1090 268 269 98.6 0.1090 128.4865 > 0.1090 387 388 90.0 0.1090 0.2040 0.1090Back Off! I just > backed up step0b.pdb to ./#step0b.pdb.18#Back Off! I just backed up > step0c.pdb to ./#step0c.pdb.18#Wrote pdb files with previous and current > coordinatesStep 0, time 0 (ps) LINCS WARNINGrelative constraint deviation > after LINCS:rms 124.010127, max 1163.317261 (between atoms 268 and > 269)bonds that rotated more than 30 degrees: atom 1 atom 2 angle > previous, current, constraint length 118 119 90.0 0.1090 > 0.1942 0.1090 264 265 90.0 0.1090 0.1964 0.1090 > 268 269 90.0 0.1090 126.9106 0.1090 387 388 90.0 > 0.1090 0.2036 0.1090Back Off! I just backed up step0b.pdb to > ./#step0b.pdb.19#Back Off! I just backed up step0c.pdb to > ./#step0c.pdb.19#Wrote pdb files with previous and current > coordinatesSegmentation fault: 11* > > Can anyone help? any suggestions are very much welcomed. > > Thank You > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.