[gmx-users] Problem with freeze groups

[Ondrej Kroutil]

Hi gromacs users again,
I have a problem with freezing of the atoms in my simulations.
I have prepared kaolinite surface and have tried to run NVT simulation (see
attached mdp file) with frozen outer layers (BULK section in my index
file). I run it with GPU.
While in 2016.5 version everything works properly, in 2018.1 I see that in
outer layers bond distances and angles are completely frozen but slabs as a
whole move. See multiple .gro file in link:

https://drive.google.com/file/d/0Byl8CD_rdzQOenVXUGlkWFZKMHlkR1BmVjB3bnYwcERZNEVR/view?usp=sharing
https://drive.google.com/file/d/0Byl8CD_rdzQOLVc5RTZTeUg1dkpjQUJlaFZpbXM4eFFTdENj/view?usp=sharing

Please, what do you think about it? Is it a bug or my bad compilation or
bad input setting?

Thank a lot and have a nice day.

    Ondřej Kroutil

https://scholar.google.cz/citations?user=vFX-JpoAAAAJ&hl=cs

P.S. Here is the beginning of my log file...

Command line:
  gmx mdrun -nt 6 -deffnm nvt-prod

GROMACS version:    2018.1
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        CUDA
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.4-sse2-avx
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
Built on:           2018-05-10 11:29:37
Built by:           mrdizzy at otto [CMAKE]
Build OS/arch:      Linux 3.16.0-4-amd64 x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
Build CPU family:   6   Model: 94   Stepping: 3
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /usr/bin/cc GNU 4.9.2
C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler:       /usr/bin/c++ GNU 4.9.2
C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
CUDA compiler:      /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=
compute_30,code=sm_30;-gencode;arch=compute_35,code=
sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=
compute_50,code=sm_50;-gencode;arch=compute_52,code=
sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;;
;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-
loops;-fexcess-precision=fast;
CUDA driver:        8.0
CUDA runtime:       7.50


Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
    Family: 6   Model: 94   Stepping: 3
    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel
lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Basic
    Sockets, cores, and logical processors:
      Socket  0: [   0   4] [   1   5] [   2   6] [   3   7]
  GPU info:
    Number of GPUs detected: 1
    #0: NVIDIA GeForce GTX 1070, compute cap.: 6.1, ECC:  no, stat:
compatible


-- 
Ondřej Kroutil
        ,,              Faculty of Science
   ----"))'             University of South Bohemia
     OOO           Branisovska 1760, Ceske Budejovice, 370 05
      OOO          The Czech Republic
        | OO         E-mail:  okroutil at gmail.com
>------    O         Mobile:  +420 736 537 190