[gmx-users] RB-coefficients of dihedral angles of triethyl phosphate itp
Rana Ali
ranadeepu2017 at gmail.com
Mon Feb 20 10:08:31 CET 2017
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)
Warm regards
Rana
On Mon, Feb 20, 2017 at 11:57 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:
> On 20/02/17 07:19, Rana Ali wrote:
>
>> Dear Sir
>> I have downloaded the itp file of triethyl phospathe and have run it
>> successfully.
>>
> Downloaded from where?
>
> You can find the dihedral coefficient by running
> gmx dump -s topol.tpr
> on your file.
>
>
>> Could you please help me how to find out the RB coefficients (c0, c1, c2,
>> c3, c4, c5) for dihedral angle given in the itp file which is given
>> below.
>> [ dihedrals ]
>> ; ai aj ak al funct c0 c1
>> c2 c3 c4 c5
>> 2 1 5 6 3
>> 2 1 5 7 3
>> 2 1 5 8 3
>> 3 1 5 6 3
>> 3 1 5 7 3
>> 3 1 5 8 3
>> 4 1 5 6 3
>> 4 1 5 7 3
>> 4 1 5 8 3
>> 1 5 8 9 3
>> 6 5 8 9 3
>> 7 5 8 9 3
>> 5 8 9 10 3
>> 5 8 9 18 3
>> 5 8 9 19 3
>> 8 9 10 11 3
>> 18 9 10 11 3
>> 19 9 10 11 3
>> 8 9 19 20 3
>> 10 9 19 20 3
>> 18 9 19 20 3
>> 9 10 11 12 3
>> 9 10 11 13 3
>> 9 10 11 14 3
>> 10 11 14 15 3
>> 10 11 14 16 3
>> 10 11 14 17 3
>> 12 11 14 15 3
>> 12 11 14 16 3
>> 12 11 14 17 3
>> 13 11 14 15 3
>> 13 11 14 16 3
>> 13 11 14 17 3
>> 9 19 20 21 3
>> 9 19 20 22 3
>> 9 19 20 23 3
>> 19 20 23 24 3
>> 19 20 23 25 3
>> 19 20 23 26 3
>> 21 20 23 24 3
>> 21 20 23 25 3
>> 21 20 23 26 3
>> 22 20 23 24 3
>> 22 20 23 25 3
>> 22 20 23 26 3
>> Thank you in advance
>>
>> Warm regards
>>
>> Rana
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
> --
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