[gmx-users] RB-coefficients of dihedral angles of triethyl phosphate itp

[Justin Lemkul]

On 2/20/17 4:08 AM, Rana Ali wrote:
> Dear Sir
> After running the gmx dump -s topol.tpr
>
> I am getting the following output. How to get the RB coefficients (c0, c1,
> c2, c3, c4, c5) for dihedral angle
>
>   x (26x3):
>    x[    0]={ 1.45500e+00,  1.43400e+00,  1.14700e+00}
>    x[    1]={ 1.42200e+00,  1.33400e+00,  1.17600e+00}
>    x[    2]={ 1.41700e+00,  1.47600e+00,  1.05400e+00}
>    x[    3]={ 1.56400e+00,  1.42900e+00,  1.15500e+00}
>    x[    4]={ 1.39300e+00,  1.52200e+00,  1.25600e+00}
>    x[    5]={ 1.28500e+00,  1.51200e+00,  1.26600e+00}
>    x[    6]={ 1.41300e+00,  1.62500e+00,  1.22600e+00}
>    x[    7]={ 1.46800e+00,  1.49400e+00,  1.37200e+00}
>    x[    8]={ 1.44300e+00,  1.56800e+00,  1.51200e+00}
>    x[    9]={ 1.58800e+00,  1.58100e+00,  1.58100e+00}
>    x[   10]={ 1.67300e+00,  1.69000e+00,  1.55500e+00}
>    x[   11]={ 1.62500e+00,  1.78500e+00,  1.57800e+00}
>    x[   12]={ 1.69500e+00,  1.69000e+00,  1.44800e+00}
>    x[   13]={ 1.79700e+00,  1.67400e+00,  1.64200e+00}
>    x[   14]={ 1.79200e+00,  1.65000e+00,  1.74900e+00}
>    x[   15]={ 1.85600e+00,  1.59200e+00,  1.60000e+00}
>    x[   16]={ 1.85800e+00,  1.76400e+00,  1.63300e+00}
>    x[   17]={ 1.38300e+00,  1.70300e+00,  1.50100e+00}
>    x[   18]={ 1.35100e+00,  1.47300e+00,  1.60400e+00}
>    x[   19]={ 1.39300e+00,  1.34200e+00,  1.63500e+00}
>    x[   20]={ 1.49100e+00,  1.35400e+00,  1.68100e+00}
>    x[   21]={ 1.39700e+00,  1.27400e+00,  1.55000e+00}
>    x[   22]={ 1.32300e+00,  1.26700e+00,  1.74800e+00}
>    x[   23]={ 1.31900e+00,  1.33900e+00,  1.83000e+00}
>    x[   24]={ 1.22000e+00,  1.23800e+00,  1.72500e+00}
>    x[   25]={ 1.38900e+00,  1.18700e+00,  1.78100e+00}
> v (26x3):
>    v[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    3]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    4]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    5]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    6]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    7]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    8]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[    9]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   10]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   11]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   12]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   13]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   14]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   15]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   16]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   17]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   18]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   19]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   20]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   21]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   22]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   23]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   24]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>    v[   25]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> Group statistics
> T-Coupling  :      26  (total 26 atoms)
> Energy Mon. :      26  (total 26 atoms)
> Acceleration:      26  (total 26 atoms)
> Freeze      :      26  (total 26 atoms)
> User1       :      26  (total 26 atoms)
> User2       :      26  (total 26 atoms)
> VCM         :      26  (total 26 atoms)
> XTC         :      26  (total 26 atoms)
> Or. Res. Fit:      26  (total 26 atoms)
> QMMM        :      26  (total 26 atoms)
>

There should be a whole lot more information in the dump of a .tpr file beyond 
simply the coordinates and velocities.  This is just the tail end of the output.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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