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

[Tanping Li]

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.


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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