[gmx-users] How to get the c12 in LJ?

[David]

On Fri, 2005-07-15 at 15:27 -0700, Tanping Li wrote:
> Thank you so much. I get the correct matrix now.
> My problem is: I want to calculate the interaction
> between the protein resdiue and the close waters.
> for the LJ part, I can't obtain the same result with
> Gromacs now matter how I try.
> 
> I use the shift function in LJ part. If I transfer to
> the cutoff, everything is fine; but for shift, there
> is always some difference between my result and
> gromacs. The shift function I used coming from
> the mannuel:
> 
> 
>     -A/3*(r*r*r)-B/4*(r*r*r*r)-C
> 
> Does gromacs use this shift function in LJ? I hope
> I did not use the wrong function.
If you select vdw_type = shift it does.
You can run mdrun -debug for a few steps and it will dump the tables
used for the potential.

> 
> 
> Best
> Tanping
> 
> 
> 
> 
> 
> --- David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 
> > On Thu, 2005-07-14 at 07:20 -0700, Tanping Li wrote:
> > > Thank you very much for the reply. But there are
> > only
> > > over 200 items in idef. How are they ordered? What
> > > does n mean here? Because there are about 50 atom
> > > types in the ***.atp file.
> > grompp removes the unused ones. you can have it not
> > do that by an option
> > -norenum
> > > 
> > > 
> > > Best
> > > Tanping
> > > 
> > > --- David van der Spoel <spoel at xray.bmc.uu.se>
> > wrote: 
> > > 
> > > > On Wed, 2005-07-13 at 14:57 -0700, Tanping Li
> > wrote:
> > > > > Hellow, everyone,
> > > > > 
> > > > > 
> > > > > I am calculating the LJ interaction between
> > > > protein
> > > > > residue and some close waters. I noticed that
> > > > > c12(i,j)=sqrt(c12(i,i)*c12(j,j)) is not always
> > > > true in
> > > > > some situations, which is also mentioned in
> > > > previous
> > > > > messages. So where can I get the c12 that
> > gromacs
> > > > > uses?
> > > > In the tpr file, there is a matrix (look for
> > idef
> > > > when you gmxdump it).
> > > > The matrix is stored linearly like 0,0 0,1, 0,2
> > ...
> > > > 1,0 1,1 ... n-1,n-1
> > > > > I have struggled for several days and hope
> > your
> > > > reply.
> > > > > Thank you very much.
> > > > > 
> > > > > 
> > > > > Best
> > > > > Tanping
> > > > >
> > _______________________________________________
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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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> > -- 
> > 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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-- 
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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