[gmx-users] Re: Re:[gmx-users] box of methanol

[nicolis at guideo.fr]

Hello again,
so, I installed the 3.1.4, looked at the opls files and added a methanol 
residue in the ffopls.rtp. After I used pdb2gmx on a gro file with the same 
atoms I defined in the rtp.
The reason I passed from the rtp/pdb2gmx was to be sure to not forgot an 
angle.
As Erik in your mail you wrote about dihedrals, I presume you had in mind an 
all atom CH3 and a united one, so that's what I used.
At the end of the mail I paste my final itp file. The minimisation results look 
like methanol :-) and I am running a MD in a 3x3x3 box to see if I get now a 
better value for the density. I let you know and if it's OK I'll send the 
equilibrated box.
But, would it not be more time efficient to use some constraints on the CH3? 
If yes how?
Thanks again,
Yiannis

On samedi, juillet 13, 2002, at 11:36 , David wrote:

>On Fri, 2002-07-12 at 23:04, Erik Lindahl wrote:

>>You might also want to try OPLS, but there's no methanol topology there
>>yet, so it has
>>to be handcoded (with all dihedrals).
>Please do that, and report the resulting topology back to the list (or
>upload to the gromacs website


; methanol_opls.itp

[ moleculetype ]
; Name            nrexcl
methanol             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      
massB
     1   opls_157      1   MeOH      C      1      0.145     12.011   ; qtot 0.145
     2   opls_156      1   MeOH     HA      1       0.04      1.008   ; qtot 0.185
     3   opls_156      1   MeOH     HB      1       0.04      1.008   ; qtot 0.225
     4   opls_156      1   MeOH     HC      1       0.04      1.008   ; qtot 0.265
     5   opls_154      1   MeOH      O      1     -0.683    15.9994   ; qtot -0.418
     6   opls_155      1   MeOH      H      1      0.418      1.008   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     4     1 
    1     5     1 
    5     6     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    2     1     4     1 
    2     1     5     1 
    3     1     4     1 
    3     1     5     1 
    4     1     5     1 
    1     5     6     1 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            
c5
    2     1     5     6     3 
    3     1     5     6     3 
    4     1     5     6     3