GROMACS version:2018

GROMACS modification: Yes/No

Here post your question

gmx mdrun -v -deffnm em

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Compiled SIMD: None, but for this host/run AVX2_256 might be better (see log).

The current CPU can measure timings more accurately than the code in

gmx mdrun was configured to use. This might affect your simulation

speed as accurate timings are needed for load-balancing.

Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.

Reading file em.tpr, VERSION 2018 (single precision)

No option -multi

Using 1 MPI thread

Using 8 OpenMP threads

WARNING: Using the slow plain C kernels. This should

not happen during routine usage on supported platforms.

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Polak-Ribiere Conjugate Gradients:

Tolerance (Fmax) = 1.50000e+03

Number of steps = 5000000

F-max = 1.07138e+12 on atom 1627

F-Norm = 2.29910e+10

Step 0, Epot=3.230856e+09, Fnorm=4.819e+09, Fmax=1.394e+11 (atom 1643)

Step 1, Epot=2.299594e+09, Fnorm=3.046e+09, Fmax=8.879e+10 (atom 1643)

Step 2, Epot=1.871346e+09, Fnorm=2.331e+09, Fmax=6.698e+10 (atom 1643)

Step 3, Epot=1.374672e+09, Fnorm=1.549e+09, Fmax=4.331e+10 (atom 1643)

Step 4, Epot=1.059982e+09, Fnorm=1.108e+09, Fmax=3.054e+10 (atom 1643)

Step 5, Epot=7.814666e+08, Fnorm=7.504e+08, Fmax=2.020e+10 (atom 1643)

Step 6, Epot=5.834828e+08, Fnorm=5.244e+08, Fmax=1.406e+10 (atom 1643)

Step 7, Epot=4.235868e+08, Fnorm=3.567e+08, Fmax=9.443e+09 (atom 1643)

Step 8, Epot=3.070316e+08, Fnorm=2.432e+08, Fmax=6.435e+09 (atom 1643)

Step 9, Epot=2.194594e+08, Fnorm=1.627e+08, Fmax=4.227e+09 (atom 1643)

Step 10, Epot=1.570532e+08, Fnorm=1.087e+08, Fmax=2.774e+09 (atom 1643)

Step 11, Epot=1.119821e+08, Fnorm=7.208e+07, Fmax=1.773e+09 (atom 1643)

Step 12, Epot=8.002037e+07, Fnorm=4.794e+07, Fmax=1.134e+09 (atom 1643)

Step 13, Epot=5.708226e+07, Fnorm=3.183e+07, Fmax=7.144e+08 (atom 1643)

Step 14, Epot=4.074676e+07, Fnorm=2.115e+07, Fmax=4.542e+08 (atom 1247)

Step 15, Epot=2.909117e+07, Fnorm=1.401e+07, Fmax=2.946e+08 (atom 1247)

Step 16, Epot=2.083233e+07, Fnorm=9.278e+06, Fmax=1.905e+08 (atom 1247)

Step 17, Epot=1.496813e+07, Fnorm=6.147e+06, Fmax=1.226e+08 (atom 1247)

Step 18, Epot=1.079560e+07, Fnorm=4.084e+06, Fmax=7.859e+07 (atom 1247)

Step 19, Epot=7.805438e+06, Fnorm=2.721e+06, Fmax=5.010e+07 (atom 1247)

Step 20, Epot=5.652430e+06, Fnorm=1.817e+06, Fmax=3.217e+07 (atom 1029)

Step 21, Epot=4.095803e+06, Fnorm=1.215e+06, Fmax=2.188e+07 (atom 1029)

Step 22, Epot=2.968536e+06, Fnorm=8.135e+05, Fmax=1.481e+07 (atom 1029)

Step 23, Epot=2.150422e+06, Fnorm=5.451e+05, Fmax=9.952e+06 (atom 1029)

Step 24, Epot=1.555052e+06, Fnorm=3.658e+05, Fmax=6.630e+06 (atom 1029)

Step 25, Epot=1.119857e+06, Fnorm=2.462e+05, Fmax=4.383e+06 (atom 1029)

Step 26, Epot=7.993461e+05, Fnorm=1.666e+05, Fmax=2.882e+06 (atom 1029)

Step 27, Epot=5.598636e+05, Fnorm=1.138e+05, Fmax=1.893e+06 (atom 1029)

Step 28, Epot=3.774210e+05, Fnorm=7.828e+04, Fmax=1.247e+06 (atom 1029)

Step 29, Epot=2.369534e+05, Fnorm=5.399e+04, Fmax=8.796e+05 (atom 744)

Step 30, Epot=1.289057e+05, Fnorm=3.717e+04, Fmax=6.107e+05 (atom 744)

Step 31, Epot=4.626921e+04, Fnorm=2.549e+04, Fmax=4.173e+05 (atom 983)

Step 32, Epot=-1.642341e+04, Fnorm=1.744e+04, Fmax=2.799e+05 (atom 983)

Step 33, Epot=-6.411712e+04, Fnorm=1.201e+04, Fmax=1.837e+05 (atom 983)

Step 34, Epot=-1.013353e+05, Fnorm=8.406e+03, Fmax=1.188e+05 (atom 983)

Step 35, Epot=-1.313058e+05, Fnorm=5.950e+03, Fmax=8.340e+04 (atom 1247)

Step 36, Epot=-1.558091e+05, Fnorm=4.232e+03, Fmax=5.867e+04 (atom 1247)

Step 37, Epot=-1.759417e+05, Fnorm=3.002e+03, Fmax=4.576e+04 (atom 1247)

Step 38, Epot=-1.921374e+05, Fnorm=2.096e+03, Fmax=2.971e+04 (atom 1247)

Step 39, Epot=-2.045221e+05, Fnorm=1.501e+03, Fmax=2.753e+04 (atom 1247)

Step 40, Epot=-2.128392e+05, Fnorm=2.220e+03, Fmax=8.603e+04 (atom 707)

Step 41, Epot=-2.130309e+05, Fnorm=2.132e+03, Fmax=8.083e+04 (atom 707)

Step 42, Epot=-2.134006e+05, Fnorm=1.881e+03, Fmax=6.584e+04 (atom 707)

Step 43, Epot=-2.147213e+05, Fnorm=3.070e+03, Fmax=1.144e+05 (atom 708)

Step 44, Epot=-2.147343e+05, Fnorm=3.101e+03, Fmax=1.136e+05 (atom 708)

Step 45, Epot=-2.191163e+05, Fnorm=9.878e+02, Fmax=3.092e+04 (atom 1343)

Step 46, Epot=-2.199840e+05, Fnorm=8.657e+02, Fmax=1.976e+04 (atom 1343)

Step 47, Epot=-2.210286e+05, Fnorm=7.453e+02, Fmax=1.078e+04 (atom 1343)

Step 48, Epot=-2.223372e+05, Fnorm=6.792e+02, Fmax=7.796e+03 (atom 1247)

Step 49, Epot=-2.241242e+05, Fnorm=6.127e+02, Fmax=6.994e+03 (atom 1247)

Step 50, Epot=-2.264262e+05, Fnorm=5.402e+02, Fmax=5.626e+03 (atom 1247)

Step 51, Epot=-2.292161e+05, Fnorm=4.638e+02, Fmax=3.997e+03 (atom 744)

Step 52, Epot=-2.323968e+05, Fnorm=4.285e+02, Fmax=9.020e+03 (atom 707)

Step 53, Epot=-2.335971e+05, Fnorm=4.262e+02, Fmax=1.052e+04 (atom 708)

Step 54, Epot=-2.366034e+05, Fnorm=6.558e+02, Fmax=2.801e+04 (atom 708)

Step 55, Epot=-2.407879e+05, Fnorm=2.008e+03, Fmax=8.592e+04 (atom 707)

Step 56, Epot=-2.409638e+05, Fnorm=1.915e+03, Fmax=7.883e+04 (atom 707)

Step 57, Epot=-2.426413e+05, Fnorm=7.860e+02, Fmax=3.555e+04 (atom 1441)

Step 58, Epot=-2.443507e+05, Fnorm=3.451e+02, Fmax=6.412e+03 (atom 1441)

Step 59, Epot=-2.455093e+05, Fnorm=2.703e+02, Fmax=4.863e+03 (atom 1639)

Step 60, Epot=-2.466843e+05, Fnorm=5.576e+02, Fmax=2.309e+04 (atom 1642)

Step 61, Epot=-2.471133e+05, Fnorm=9.062e+02, Fmax=4.381e+04 (atom 1639)

Step 62, Epot=-2.472244e+05, Fnorm=3.280e+02, Fmax=1.020e+04 (atom 1627)

Step 63, Epot=-2.476386e+05, Fnorm=3.163e+02, Fmax=1.049e+04 (atom 1627)

Step 64, Epot=-2.481261e+05, Fnorm=2.894e+02, Fmax=9.361e+03 (atom 1627)

Step 65, Epot=-2.483511e+05, Fnorm=3.638e+02, Fmax=1.392e+04 (atom 1627)

Step 66, Epot=-2.483752e+05, Fnorm=5.857e+02, Fmax=2.356e+04 (atom 1627)

Step 67, Epot=-2.493838e+05, Fnorm=2.743e+02, Fmax=7.574e+03 (atom 1643)

Step 68, Epot=-2.496374e+05, Fnorm=1.567e+02, Fmax=1.829e+03 (atom 1639)

Step 69, Epot=-2.498764e+05, Fnorm=1.598e+02, Fmax=3.421e+03 (atom 1431)

Step 70, Epot=-2.502622e+05, Fnorm=2.798e+02, Fmax=1.309e+04 (atom 1431)

Step 71, Epot=-2.538323e+05, Fnorm=1.717e+03, Fmax=8.681e+04 (atom 1432)

Step 72, Epot=-2.542346e+05, Fnorm=1.691e+03, Fmax=8.526e+04 (atom 1432)

Step 73, Epot=-2.549277e+05, Fnorm=1.715e+03, Fmax=8.647e+04 (atom 1429)

Step 74, Epot=-2.550878e+05, Fnorm=1.643e+03, Fmax=8.270e+04 (atom 1432)

Step 75, Epot=-2.550992e+05, Fnorm=1.716e+03, Fmax=8.645e+04 (atom 1429)

Step 76, Epot=-2.551361e+05, Fnorm=1.637e+03, Fmax=8.236e+04 (atom 1432)

Step 77, Epot=-2.551654e+05, Fnorm=1.714e+03, Fmax=8.634e+04 (atom 1429)

Step 78, Epot=-2.551766e+05, Fnorm=1.636e+03, Fmax=8.234e+04 (atom 1432)

Step 79, Epot=-2.552027e+05, Fnorm=1.679e+03, Fmax=8.504e+04 (atom 1429)

Step 80, Epot=-2.552057e+05, Fnorm=1.627e+03, Fmax=8.172e+04 (atom 1432)

Step 81, Epot=-2.552060e+05, Fnorm=1.710e+03, Fmax=8.619e+04 (atom 1429)

Step 82, Epot=-2.552060e+05, Fnorm=1.639e+03, Fmax=8.260e+04 (atom 1432)

Energy minimization has stopped, but the forces have not converged to the

requested precision Fmax < 1500 (which may not be possible for your system).

It stopped because the algorithm tried to make a new step whose size was too

small, or there was no change in the energy since last step. Either way, we

regard the minimization as converged to within the available machine

precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not

needed for preparing to run molecular dynamics.

writing lowest energy coordinates.

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Polak-Ribiere Conjugate Gradients converged to machine precision in 82 steps,

but did not reach the requested Fmax < 1500.

Potential Energy = -2.5520603e+05

Maximum force = 8.2601156e+04 on atom 1432

Norm of force = 1.6394663e+03

Hi ,I am working on cysteine adsorption Au surface so i am tried to energy minimisation it giving this error again and again energy minimisation has stopped,i tried everything changing integrator, to emtol,rvdw still error has occuring. Pls help me I am stuck for a long time,dont know whats getting error.