[gmx-users] Ammonia in Water

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> Hello,
> 
>    I created a topology file for 1 ammonia in water. Could someone 
> please have a look at the file and let me know if it looks okay.
> 

With a fractional charge of +0.38, I'd say these parameters (at least as far as 
the charges) are inappropriate.  The only way to determine if parameters are 
appropriate is to derive them in a manner consistent with the original force 
field.  This is not a trivial task.  Consult the list archive and Gromacs wiki 
for tips.

-Justin

> Thanks
> Nisha Patel
> 
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
> Ammonia             3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> typeB    chargeB      massB
>      1   opls_237      1    NH3      N      1      -0.76    14.0067   ; 
> qtot -0.76
>      2   opls_240      1    NH3     H1      1       0.38      1.008   ; 
> qtot -0.38
>      3   opls_240      1    NH3     H2      1       0.38      1.008   ; 
> qtot 0
>      4   opls_240      1    NH3     H3      1       0.38      1.008   ; 
> qtot 0.38
> 
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     1     3     1
>     1     4     1
> 
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2      
>       c3
>     2     1     3     1
>     2     1     4     1
>     3     1     4     1
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Include water topology
> #include "spc.itp"
> 
> 
> [ system ]
> ; Name
> ammonia in water
> 
> [ molecules ]
> ; Compound        #mols
> Ammonia             1
> SOL               345
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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