[gmx-users] Re: Tabulated G96 Angle potential

[Nicu]

Nicu wrote:
> Dear all,
>
> I try to match a Martini angle potential (g96) for a CG HD with a 
> tabulated one. All the other tabulated potentials that I constructed 
> for  bonds and  nonbonded  work fine.  But for angle it  does not  go 
> well (the entropy drops from 176 to 100). I put bellow the PYTHON 
> script that computes the values for this potential and the definition 
> of HD angle potential in Martini. Do I do a stupid mistake? Or is 
> something else. I use gromacs 4.0.2. Attached also a fragment of the 
> angle tabulated potential (table_a1.xvg)
>
> HD ....
> [angles]
> ; i j k         funct   angle   force.c.
>  1 2 3         2       180.0   25.0
>  2 3 4         2       180.0   25.0
>
> PYTHON SCRIPT
> potential = []
> r = 0
> value = 0
> for i in range(4000):
>        if r > 0.001:
>                array = [ 0, 0]
>                value = 0.5*25*(math.pow((math.cos(r)- math.cos(180)), 
> 2 ))
>                print r , value
>
>        r = r + 0.045
>
>
>
> minnu vijayan wrote:
>> hello friends
>> for doing normal mode analysis i am trying to create .mtx file .but 
>> in output i am not getting thi .mtx file..what all precautions i have 
>> to take
>>  
>> with thanks
>>
>>
>>  
>
> ------------------------------------------------------------------------
>
> 0.045 31.8979910216 500.0
> 0.09 31.7769022926 3.57911403889
> 0.135 31.5758707581 5.34263731333
> 0.18 31.2960649344 7.07513304778
> 0.225 30.9391087838 8.76661186444
> 0.27 30.5070698666 10.4073834889
> 0.315 30.0024442698 11.9881270889
> 0.36 29.4281384286 13.4999587078
> 0.405 28.7874479861 14.9344952478
> 0.45 28.0840338563 16.2839145311
> 0.495 27.3218956783 17.5410109444
> 0.54 26.5053428713 18.6992462311
> 0.585 25.6389635175 19.7527950567
> 0.63 24.7275913162 20.6965849744
> 0.675 23.7762708698 21.5263304878
> 0.72 22.7902215723 22.2385609456
> 0.765 21.7748003847 22.8306420678
> 0.81 20.7354637862 23.3007909289
> 0.855 19.6777292011 23.6480842933
> 0.9 18.6071361998 23.8724602578
> 0.945 17.5292077779 23.9747131822
> 0.99 16.4494120134 23.9564819756
> 1.035 15.3731244001 23.8202318322
> 1.08 14.3055911485 23.5692295933
> 1.125 13.2518937367 23.2075129144
>