[gmx-users] RB-coefficients of dihedral angles of triethyl phosphate itp
Rana Ali
ranadeepu2017 at gmail.com
Mon Feb 20 14:49:43 CET 2017
Dear David and Justin
Thank you both for helping me out of the problem. We have got the desired
RB coefficients.
Warm regards
Rana
On Mon, Feb 20, 2017 at 6:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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