[gmx-users] 3.3 release and Forcefield nb.itp format

[David]

On Wed, 2005-10-19 at 02:34 +0800, Yang Ye wrote:
> After checking, I found that grompp has used comb-rule 1 for
> generating LJ.
So problem solved?


> 
> Yang Ye
> 
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>    1            3               no                0.5   0.833333
> 
> Erik Lindahl wrote: 
> > Hi Yang, 
> > 
> > Please include the header [defaults] section from your forcefield. 
> > 
> > The number of columns is flexible, since both atomic number and
> > bonded_atomtype fields are optional. 
> > 
> > Cheers, 
> > 
> > Erik 
> > 
> > On Oct 18, 2005, at 7:25 PM, Yang Ye wrote: 
> > 
> > > Hi, 
> > > 
> > > I have found that 3.3's grompp generates drastically different
> > > LJ_SR and LJ14 parameters for one of my self-defined forcefield
> > > (converted from AMBER). 
> > > 
> > > >From gmxdump, 
> > > (3.3's tpr) tpx version 40 
> > >         ntypes=72 
> > >            functype[0]=LJ_SR, c6= 2.24468820e-20, c12=
> > > 3.18825866e-35 
> > >            functype[1]=LJ_SR, c6= 1.61870333e-32, c12= 0.00000000e
> > > +00 
> > >            functype[2]=LJ_SR, c6= 1.43123863e-20, c12=
> > > 1.22953165e-35 
> > >            functype[3]=LJ_SR, c6= 1.17580789e-26, c12= 0.00000000e
> > > +00 
> > >            ... 
> > > 
> > > They should be 
> > > (3.3b's tpr) tpx version 32 
> > >         ntypes=72 
> > >            functype[0]=LJ_SR, c6= 3.35273775e-03, c12=
> > > 3.95092275e-06 
> > >            functype[1]=LJ_SR, c6= 8.76983977e-05, c12=
> > > 8.89523299e-09 
> > >            functype[2]=LJ_SR, c6= 3.08322068e-03, c12=
> > > 4.16509010e-06 
> > >            functype[3]=LJ_SR, c6= 4.73846623e-04, c12=
> > > 2.59686658e-07 
> > >            ... 
> > > 
> > > My ffambernb.itp is 
> > > [ atomtypes ] 
> > > ;name        mass      charge   ptype            c6           c12 
> > >     H     1.008     0.000     A  3.9229141156e-07
> > > 5.8568793913e-13 
> > >    HO     1.008     0.000     A  0.0000000000e+00  0.0000000000e
> > > +00 
> > > ... 
> > > [ nonbond_params ] 
> > > ; i    j func          c6           c12 
> > >     H     H   1  3.9229141156e-07  5.8568793913e-13 
> > >     H    HO   1  0.0000000000e+00  0.0000000000e+00 
> > >     H    HS   1  3.9229141156e-07  5.8568793913e-13 
> > > ... 
> > > [ nonbond_params ] 
> > > ; i    j func          c6           c12 
> > >     H     H   1  3.9229141156e-07  5.8568793913e-13 
> > >     H    HO   1  0.0000000000e+00  0.0000000000e+00 
> > >     H    HS   1  3.9229141156e-07  5.8568793913e-13 
> > > ... 
> > > 
> > > I found that FF provided by gromacs has different column width. Is
> > > this the reason? 
> > > 
> > > Thanks. 
> > > 
> > > Yang Ye 
> > > 
> > > _______________________________________________ 
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> > > 
> > > 
> > 
> > ----------------------------------------------------------- 
> > Erik Lindahl  <lindahl at sbc.su.se> 
> > Assistant Professor, Stockholm Bioinformatics Center 
> > Stockholm University, SE 106 91 Stockholm 
> > Phone: +46 8 5537 8564     Fax: +46 8 5537 8214 
> > 
> > 
> > 
> > 
> > _______________________________________________ 
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> > 
> 
> -- 
> Regards,
> Yang Ye
> Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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