[gmx-users] ethanol bond types

[David van der Spoel]

On 3/3/10 8:14 PM, nishap.patel at utoronto.ca wrote:
> Hello,
>
>     I am trying to simulate Ethanol in water using OPLSAA. I already 
> tried it with all atoms, but now I want to try it with United atoms 
> for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I created 
> the topology but I got an error saying 'No bond types', so I checked 
> ffoplsaabon.itp file, and as the error indicated I could not find any 
> bond types. Is there a way for me to determine the bonds? This is my 
> topology file for ethanol:
>
> [ moleculetype ]
> ; Name            nrexcl
> Ethanol             3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1   opls_068      1    EOH     CB      1          0     15.035   
> ; qtot 0
>      2   opls_081      1    EOH     CA      2      0.265     14.027   
> ; qtot 0.265
>      3   opls_078      1    EOH     OH      2       -0.7    15.9994   
> ; qtot -0.435
>      4   opls_079      1    EOH     HO      2      0.435      1.008   
> ; qtot 0
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     2     3     1
>     3     4     1
>
> [ pairs ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     4     1
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2      
>       c3
>     1     2     3     1
>     2     3     4     1
>
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            
> c2            c3            c4            c5
>     1     2     3     4     3
>
> I checked one of the paper that has been published using the same 
> parameters as follows:
>
>    Table 1. Potential Parameters and Molecular
>          Geometries of OPLS-UA and SPC/E
>                                              qa
> atom or group       ?, Å      , kJ/mol
>                          OPLS
>      R1            3.905      0.7322        0.000
>      R2            3.905      0.4937        0.265
>                                           -0.700
>      O             3.070      0.7113
>      H             0.000      0.0000        0.435
>
> I would really appreciate some suggestions, on how I should tackle the 
> error.
>
> Thanks
>
> Nisha P
>
>
The united atom parameters are really leftovers from long past. 
Jorgensen published his first all-atom alcohol simulations in 1988 IIRC. 
There is a methanol paper from 1983. Just search literature for 
Jorgensen, methanol ethanol and it will show up. Then you will to type 
in the parameters yourself, see chapter 5.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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