How to compile the hypersound-perturbed MD program. 

(i): Type “git clone https://github.com/clinfo/gromacs.git“ and change to “gromacs”.

(ii): Type “git checkout hypersound”.

(iii): Following three files (“md.c”, “repl_ex.c”, and “repl_ex.h”) have been modified to model hypersound shock waves irradiated to solvent molecules. Prior to compilation, you have to change the "N", "vmax", and "Tint" parameters, which are defined in Fig. 1A, and "the starting atom number for solvent atoms" and "the side length of a cubic box" appropriate for your simulation system.

<src/kernel/md.c>
line2072, 2073: setting of the N value

< src/kernel/repl_ex.c>
line1401: setting of the starting atom number for solvent atoms [corresponding to “6549” in case of Ref.gro (CDK2-CS3 system)]
line1402: setting of the side length of a cubic box (nm) [corresponding to “8.4” in case of Ref.gro (CDK2-CS3 system)]
line1423: setting of time intervals between shock wave generation (Tint)
line1469, 1480, 1492, 1503, 1515, 1527: setting of the maximum velocity (vmax)

< src/kernel/repl_ex.h>

(iv): Make a separate build directory (e.g. build_test), and change to it.

(v): Run “cmake” with the path to the source as an argument.
(e.g. cmake .. -DCMAKE_INSTALL_PREFIX=/home/apps/gromacs-4.6.5 -DGMX_MPI=OFF -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-8.0)

(vi): Change to “build_test/src/kernel” and type "make mdrun".

(vii): You will see a binary file of “mdrun”, which can be used for the hypersound-perturbed MD simulation.
### Ref.gro ###
Protein in water
60120
    1MET      N    1   5.928   4.496   6.659
    1MET     H1    2   5.927   4.588   6.702
    1MET     H2    3   5.984   4.437   6.719
    1MET     H3    4   5.975   4.505   6.570
…

  298LEU   HD21 4843   3.236   4.247   5.860
  298LEU   HD22 4844   3.325   4.144   5.976
  298LEU   HD23 4845   3.169   4.092   5.911
  298LEU      C 4846   3.092   3.944   6.311
  298LEU    OC1 4847   3.196   3.886   6.348
  298LEU    OC2 4848   2.988   3.945   6.380
  299LIG    CAI 4849   2.955   2.867   5.210
  299LIG    CAJ 4850   3.036   2.757   5.272
  299LIG    CAT 4851   2.985   2.869   5.357
  299LIG    CAS 4852   2.882   2.838   5.457
  299LIG    CAH 4853   2.778   2.753   5.439
…
348LIG    HAG 6545   5.047   5.729   1.508
  348LIG    HAE 6546   4.851   5.604   1.574
  348LIG   HAA1 6547   4.604   5.243   1.420
  348LIG   HAA2 6548   4.702   5.291   1.284
  349SOL     OW 6549   0.579   1.302   1.205
  349SOL    HW1 6550   0.497   1.301   1.156
  349SOL    HW2 6551   0.590   1.394   1.231
  350SOL     OW 6552   1.585   1.512   0.709
…
18277CL      CL60117   7.781   4.706   5.494
18278CL      CL60118   8.037   6.695   7.848
18279CL      CL60119   8.326   7.422   6.107
18280CL      CL60120   0.059   7.912   7.476
   8.43544   8.43544   8.43544

#######################################################################################################
The following is the original GROMSCS README.
#######################################################################################################

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