[gmx-users] 1-4 Interactions

[toma0052]

Hi,
     Thanks for the prompt responses.  I checked the distance between atoms
908 and 913 in VMD and got 0.396nm, which seems fine.  I thought then, that
my problem may be with my box size when I used editconf.  When I changed
the box dimension to 2.0nm from the molecule periphery, the warning between
atoms 908 and 913 disappeared.  However, I then recieved a similar error 

warning: interaction between 911 and 932 at distance 6.244 which is larger
than the 1-4 table size 1.000 nm

I checked atoms 911 and 932 using VMD, and they don't appear to be close at
all, and their distance is in fact 6.244nm.  Does this mean that there is a
problem with my topology file?  My topology file is the same as that given
on Tieleman's site, except that I removed #include "lipid.itp".  This was
giving me an error, and I did download the ffgmx_lipids.tar.gz file from
the Gromacs site, which seemed to solve the problem.  So, I am not sure why
this error is occuring.  The problem could be with my em.mdp file.  I am
new to Gromacs, and so I used the em.mdp file from John Kerrigan, which is
below.  If anyone has any ideas, that would be great.

Thanks,
Mike Tomasini

em.mdp

title		    =  DPPC
cpp                 =  /lib/cpp
define              =  -DFLEXIBLE
constraints         =  none
integrator          =  steep
dt		    =  0.002	; ps
nsteps              =  400
nstlist		    =  5
ns_type             =  grid
pbc		    =  full
rlist               =  0.9
table-extension	    =  1
coulombtype	    =  PME
rcoulomb            =  0.9
rvdw                =  1.4
fourierspacing		=  0.12
fourier_nx	    =  0
fourier_ny	    =  0
fourier_nz	    =  0
pme_order	    =  4
ewald_rtol	    =  1e-5
optimize_fft		  =  yes
;
;	Energy minimizing stuff
;
emtol               =  1000
emstep              =  0.01






On 19 Oct 2006, Tsjerk Wassenaar wrote:
> Hi Mike,
> 
> A 1-4 interaction is an interaction between two atoms which are
> attached to each other with three bonds in between (two other atoms,
> 1-2-3-4). Based on the normal bond lengths, angles, etc. two such
> atoms should not be further away from each other than 1 nm. Check the
> atom locations of 908 and 913 in a viewer and try to see what is wrong
> (also check the topology and the box).
> 
> Best,
> 
> Tsjerk
> 
> On 10/19/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > toma0052 wrote:
> > > Hello,
> > >      I am starting simulations on a DPPC lipid bilayer taken from
Peter
> > > Tieleman's website.  Upon trying to run the energy minimization, the
> > > program runs, but the results does not appear correct.  During the
run, I
> > > get the warning:
> > >
> > > Warning: 1-4 interaction between 908 and 913 at distance 1.621 which
is
> > > larger than the 1-4 table size 1.000 nm.  These are ignored for the
rest
> of
> > > the simulation.  This usually means your system is exploding, if not,
you
> > > should increase table-extension in your mdp file.
> > >
> > > I have tried increasing the table-extension in my em.mdp file, but I
need
> > > to increase it to over 10nm in order for that error to go away. 
Could
> > > someone explain a little bit more on what the table-extension and 1-4
> > > interactions are, and what could possibly be wrong with my energy
> > > minimization.  All I have done so far is to take the dppc128.pdb file
and
> > > the example2.top topology file from Peter Tieleman's site, run
editconf
> and
> > > grompp with en em.mdp file similar to John Kerrigan's tutorial,
followed
> by
> > > mdrun.  Any help would be appreciated.
> >
> > My guess is the topology is broken, or doesn't correspond to the
> > configuration. Get out VMD or something and look at things visually.
> >
> > Mark
> > _______________________________________________
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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