[gmx-users] gromacs doubt

[manjula kasinathan]

Hi all

       i have done protein protein interaction and the complex structure was
taken for MD simulation using Gromacs. the length of the protein was around
1100 aa. while performing mdrun step for position restrain i got error. i
have carried out mdrun for 1ps and the command given for mdrun and position
restrain are

         grompp -f *.pdb -c *.gro -p top.top -o *.tpr

         mdrun -v -deffnm pr

error i got was

starting mdrun '? in water'
500 steps,      1.0 ps.
step 400, remaining runtime:   133 s
Step 416, time 0.832 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000577, max 0.008379 (between atoms 5530 and 5532)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8190   8191   30.7    0.1014   0.1000      0.1000

Step 419, time 0.838 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000874, max 0.019432 (between atoms 5526 and 5527)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    112    113   31.0    0.1017   0.1002      0.1000

Step 430, time 0.86 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 158552932798158.562500, max 14888250728513536.000000 (between atoms 1734
and 1735)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4469   4471   66.7    0.1327   0.5535      0.1330
   4469   4470   69.6    0.1227   0.5336      0.1230

  8001   8003   47.0    0.0999   0.0998      0.1000
   7995   7996   30.0    0.1001   0.0999      0.1000
   7970   7971   34.0    0.0999   0.1002      0.1000

t = 0.860 ps: Water molecule starting at atom 81142 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates


could any one pls  help me to overcome this problem.how give me some ideas.

looking forward for a solution. thanx in advance.





-- 
With Regards,

Manjulakasinathan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100513/0b069977/attachment.html>