[gmx-users] Re: gmx-users Digest, Vol 73, Issue 77

[manjula kasinathan]

hi

     i gave energy minimization for 3000 steps but it runs only 1906 steps.
these are the files (em.trr, em.edr, em.log) i got after energy
minimization. my energy values are
P.E = -2.6755090e+06
Maximum force = 9.6265039e+02 an atom 5483
Norm of force = 1.263261.9e+01

         while doing position restrain with these files i got error like

WARNING 1 [file pr.mdp, line unknown]:
  Unknown or double left-hand 'warnings' in parameter file
NOTE 1 [file top.top, line 41]:
  System has non-zero total charge: -3.400000e+01

by using -maxwarn option i ignored the warnings and gone for mdrun it gives
error like this

starting mdrun 'Protein in water'
500 steps,      1.0 ps.
step 400, remaining runtime:   150 s
Step 416, time 0.832 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000996, max 0.006287 (between atoms 5428 and 5430)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  12635  12636   30.1    0.1104   0.1093      0.1090
  10211  10213   38.3    0.1104   0.1097      0.1090

Step 423, time 0.846 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025639, max 2.318898 (between atoms 8806 and 8807)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8278   8281   31.7    0.1090   0.1090      0.1090
   7545   7546   36.4    0.1087   0.1090      0.1090

hi justin u told me to check the output configuration. i didn't get this
line could u tell me which output i have to check.
i loaded the em.gro file in vmd there is no changes in structure.

looking forward for a reply. thanks in advance.

cheers,

Manju.
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