[gmx-users] dihedral parameters in oplsaa

[friendli]

No. there is no warning in grompp.

thanks



Message: 2
Date: Tue, 27 May 2008 11:17:21 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] dihedral parameters in oplsaa
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <483BD1A1.2090305 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

friendli wrote:

> > Thanks David and Mark for the advice. But I think I did not state it 
> > very clearly.
> > 
> > It is not 9 sets of dihedrals which share the same parameters are found 
> > in the output by gmxdump. But 9 of the 15 dihedrals exist in this 
> > molecule are listed. They are under Ryckaert-Bell. As for the function 
> > types, there are only two.
> > 
> > I pastes the relevant part this time.  The missing parameter dihedrals 
> > are labeled with ; **.
>   

Then most likely they have parameters that are zero. Do you get grompp 
warnings about this?


> > 
> > from .top file,
> > [ 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     ; **
> >    1     5     8    10     3    ; **
> >    6     5     8     9     3     ; **
> >    6     5     8    10     3    ; **
> >    7     5     8     9     3     ; **
> >    7     5     8    10     3    ; **
> > ___________________________________________
> > from  gmxdump,
> >       Ryckaert-Bell.:
> >            nr: 45
> >            multinr[division over processors]: 45
> >            iatoms:
> >               0 type=47 (RBDIHS) 1 0 4 5
> >               1 type=47 (RBDIHS) 1 0 4 6
> >               2 type=48 (RBDIHS) 1 0 4 7
> >               3 type=47 (RBDIHS) 2 0 4 5
> >               4 type=47 (RBDIHS) 2 0 4 6
> >               5 type=48 (RBDIHS) 2 0 4 7
> >               6 type=47 (RBDIHS) 3 0 4 5
> >               7 type=47 (RBDIHS) 3 0 4 6
> >               8 type=48 (RBDIHS) 3 0 4 7
> > _____________________________________________
> > for identify the atom numbers,
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass  
> > typeB    chargeB      massB
> >     1   opls_287      1    GLY      N      1       -0.3    14.0067   ; 
> > qtot -0.3
> >     2   opls_290      1    GLY     H1      1       0.33      1.008   ; 
> > qtot 0.03
> >     3   opls_290      1    GLY     H2      1       0.33      1.008   ; 
> > qtot 0.36
> >     4   opls_290      1    GLY     H3      1       0.33      1.008   ; 
> > qtot 0.69
> >     5   opls_298      1    GLY     CA      1       0.09     12.011   ; 
> > qtot 0.78
> >     6   opls_140      1    GLY    HA1      1       0.06      1.008   ; 
> > qtot 0.84
> >     7   opls_140      1    GLY    HA2      1       0.06      1.008   ; 
> > qtot 0.9
> >     8   opls_271      1    GLY      C      2        0.7     12.011   ; 
> > qtot 1.6
> >     9   opls_272      1    GLY     O1      2       -0.8    15.9994   ; 
> > qtot 0.8
> >    10   opls_272      1    GLY     O2      2       -0.8    15.9994   ; 
> > qtot 0
> > 
> > 
> > regards
> > 
> > LQ
>