Re: [gmx-users] 1-4 interaction, a distance greater than table size

2010-11-14 Thread Justin A. Lemkul 



Amin Arabbagheri wrote:

Dear All,

I'm simulating a DNA duplex using amber99p. starting the simulation(step 
0) i face an error which tells:


starting mdrun 'Protein in water'
50 steps,500.0 ps.
step 0Warning: 1-4 interaction between 136 and 179 at distance 
96871502.536 which is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Segmentation fault

I've checked the distance between atoms 136 and 179, its quite normal, 
about 3 angstrom (not 96871502 !!).

Im also attaching the output (md.log) which may help finding a reason:

Started mdrun on node 0 Sun Nov 14 10:17:10 2010

   Step   Time Lambda
  00.00.0

Grid: 9 x 9 x 9 cells
   Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  LJ-14
1.77478e+026.08613e+021.86464e+021.58123e+036.34721e+02
 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
   -1.03292e+044.16184e+04   -3.45397e+05   -3.54920e+04   -3.46412e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
5.24527e+01   -3.46359e+052.90932e-01   -6.00103e+03

Maybe its necessary to say that, I'm coupling my system with both 
thermostat and barostat, using a reasonable temperature of 300K.




A complete .mdp file would be significantly more useful.  Did you do energy 
minimization?  If so, what was the outcome?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin


Thanks in advance for any instruction,
Amin




--


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


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[gmx-users] 1-4 interaction, a distance greater than table size

2010-11-13 Thread Amin Arabbagheri 
Dear All,

I'm simulating a DNA duplex using amber99p. starting the simulation(step 0) i 
face an error which tells:

starting mdrun 'Protein in water'
50 steps,    500.0 ps.
step 0Warning: 1-4 interaction between 136 and 179 at distance 96871502.536 
which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Segmentation fault

I've checked the distance between atoms 136 and 179, its quite normal, about 3 
angstrom (not 96871502 !!). 
Im also attaching the output (md.log) which may help finding a reason:

Started mdrun on node 0 Sun Nov 14 10:17:10 2010

   Step   Time Lambda
  0    0.0    0.0

Grid: 9 x 9 x 9 cells
   Energies (kJ/mol)
   Bond  Angle    Proper Dih. Ryckaert-Bell.  LJ-14
    1.77478e+02    6.08613e+02    1.86464e+02    1.58123e+03    6.34721e+02
 Coulomb-14    LJ (SR)   Coulomb (SR)   Coul. recip.  Potential
   -1.03292e+04    4.16184e+04   -3.45397e+05   -3.54920e+04   -3.46412e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    5.24527e+01   -3.46359e+05    2.90932e-01   -6.00103e+03

Maybe its necessary to say that, I'm coupling my system with both thermostat 
and barostat, using a reasonable temperature of 300K.

Thanks in advance for any instruction,
Amin



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