[gmx-users] simulation of long hydrocarbons

[Dallas Warren]

>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.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Visual of this "problem" - https://twitter.com/dr_dbw/status/909559339366572032
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 22 October 2017 at 02:23, Saeed Nasiri <s.t.nasiri at gmail.com> wrote:
> 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
> DODECANE_box.gro
>  gmx_mpi_d editconf -f DODECANE_pro.gro -o DODECANE_box.gro -c -d 1.0 -bt
> cubic
>
> 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.
> thanks
>
>
> *** insert-molecules ***
> Potential Energy  =  2.91421530260847e+01
> Maximum force     =  8.55101997869504e+00 on atom 35
> Norm of force     =  6.37158190082328e+00
>
> ***editconf***
> Potential Energy  =  2.92081220273667e+01
> Maximum force     =  9.58502180917751e+00 on atom 34
> Norm of force     =  7.63991317861568e+00
> --
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