shikha agarwal wrote:
hi,
HAPPY NEW YEAR
I am experiencing a segmentation fault during mdrun in equlibration step .
error
Wrote pdb files with previous and current coordinates
[shikha-desktop:01719] *** Process received signal ***
[shikha-desktop:01719] Signal: Segmentation fault (11)
[shikha-desktop:01719] Signal code: Address not mapped (1)
[shikha-desktop:01719] Failing at address: 0x8d22a70
[shikha-desktop:01719] [ 0] [0xb87410]
[shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789]
[shikha-desktop:01719] *** End of error message ***
Segmentation fault
bottom lines of my .log file after energy minimization is this
Step Time Lambda
11357 11357.00000 0.00000
Step Time Lambda
11358 11358.00000 0.00000
Step Time Lambda
11359 11359.00000 0.00000
Step Time Lambda
11360 11360.00000 0.00000
Step Time Lambda
11361 11361.00000 0.00000
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 11362 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -5.4871900e+06
Maximum force = 3.9830833e+03 on atom 4511
Norm of force = 1.9521437e+01
Well, EM completed, but the forces are still very high, indicating that the
system is likely not yet stable. Look at the structure to see what might be
causing problems around atom 4511.
-Justin
--
========================================
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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