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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