[gmx-users] a problem with a DNA simulation using the g53a6 forcefield

[David]

On Tue, 2005-06-07 at 07:37 -0700, Kristina Nicole Woods wrote:
> Hello all:
> 
> I am trying to do a simulation of a short fragment of double stranded DNA
> (12 base pairs) using the g53a6 forcefield.  But during the minimization
> step the DNA is pulled apart and I'm not sure what I am doing wrong.  Here
> is the .mdp file for the minimization step that I have tried using:

Are you sure it is not due to periodic boundary conditions?

> 
> ---------------------------------------------------------------------
> ;       Wed Nov  3 17:12:44 1993
> ;       Input file
> ;
> cpp                 = c:/Progra~1/gromacs/bin/cpp
> include             =  -I/cygdrive/c/DNA_normal/gromacs_dna/53a6
> -I/cygdrive/c/Progra~1/gromacs/share/top
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  100
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
> 
> coulombtype         = PME
> rvdw                = 1.4
> rlist               = 0.8
> rcoulomb            = 1.4
> fourierspacing      = 0.12
> pme_order           = 4
> ewald_rtol          = 1e-5
> 
> vdwtype             = cut-off
> pbc                 = xyz
> ns_type             = simple
> dispcorr            = enerpres
> ---------------------------------------------------------------------
> 
> I was wondering if anyone can point out any serious problems that I have
> that would cause this to happen?
> 
> I should also mention that the fragment of DNA is contained within a box
> with dimensions of 3.71 nm/3.38 nm/4.30 nm and solvated with a 0.25 nm
> shell of water.
> 
> Any help would be greatly appreciated!
> 
> Kristina :)
> 
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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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