[gmx-users] (no subject)

[César Ávila]

Dear Ainun.
It looks like your system is exploding. Check the input coordinates.
Cheers
Cesar
El 03/10/2014 01:10, "AINUN NIZAR M" <0810710019 at 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:
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> *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.
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> *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
> --
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