[gmx-users] (no subject)

[AINUN NIZAR M]

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