[gmx-users] simulation of long hydrocarbons

Saeed Nasiri s.t.nasiri at gmail.com
Sat Oct 21 17:23:24 CEST 2017

Dear all

I want to simulate a decane molecule and I used some of the parameters of a
paper. The paper studied only C-C-C-C dihedral parameter. As far As I know,
the "CT" show the carbon in the aliphatic hydrocarbons in the OPLS-AA force
field. I used the following parameters for decane (for all carbons). Please
let me know, if there is any mistakes (I am not sure) ? Is it OK to used
the parameter from different source (all of them are selected from the
OPLS-AA force field) ?

  CB    CT      1    0.15100   265265.6   ; Added DSM (from CA-CT)
  CT    HC      1    0.10900   284512.0   ; CHARMM 22 parameter file

  CT     CT     CT      1   112.700    488.273   ; CHARMM 22 parameter file
  CT     CT     HC      1   110.700    313.800   ; CHARMM 22 parameter file
  HC     CT     HC      1   107.800    276.144   ; CHARMM 22 parameter file

  CT     CT     CT     HC      3      0.62760   1.88280   0.00000
-2.51040   0.00000   0.00000 ; hydrocarbon all-atom
  HC     CT     CT     HC      3      0.62760   1.88280   0.00000
-2.51040   0.00000   0.00000 ; hydrocarbon *new* 11/99

The next question is about the "insert-molecules" and "editconf" commands.
I used the following commands:

 gmx_mpi_d insert-molecules -ci  DODECANE_pro.gro -nmol 1 -box 3 3 3 -o
 gmx_mpi_d editconf -f DODECANE_pro.gro -o DODECANE_box.gro -c -d 1.0 -bt

When I used the " editconf " the equilibration step is OK, but the "
insert-molecules " command generate a box which the molecule is at the
corner of  the box and after equilibration step some parts of the molecule
are at the opposite site. The results of the equilibration steps for both
commands are shown as follows. Please tell me more about this problem!
 Any help will highly appreciated.

*** insert-molecules ***
Potential Energy  =  2.91421530260847e+01
Maximum force     =  8.55101997869504e+00 on atom 35
Norm of force     =  6.37158190082328e+00

Potential Energy  =  2.92081220273667e+01
Maximum force     =  9.58502180917751e+00 on atom 34
Norm of force     =  7.63991317861568e+00

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