[gmx-users] energy minimization of DNA in water

[David]

On Sun, 2005-08-07 at 14:18 -0700, Kristina Woods wrote:
> Hi there,
> 
> I have been trying to minimze a fragment of DNA in water for a normal
> mode analysis...but without much luck.
> 
> I am using a .mdp file for the energy minimization that looks like this:
> -----------------------------------------------------------------------
> cpp                 = /usr/bin/cpp
> include             =  -I/usr0/user/kwoods/gromacs/DNA_normal/53a6
> -I/usr0/user/kwoods/gromacs/gromacs-3.2.1/share/top
> define              =  -DFLEXIBLE
> integrator          =  cg
> constraints         =  none
> nsteps              =  500000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  0.00001
> emstep              =  0.00001
> nstcgsteep          =  100        
> coulombtype         = PME
> rvdw                = 1.4
> rlist               = 1.4 
> rcoulomb            = 1.4 
> fourierspacing      = 0.12 
> pme_order           = 4
> ewald_rtol          = 1e-5
> vdwtype             = shift
> ns_type             = grid
> dispcorr            = enerpres
> nstxout             = 50
> xtc_grps            = system
> energygrps          = system
> nstlist             = 10
> -----------------------------------------------------------------------
> 
> But here are the lowest energy coordinates that I can achieve:
> 
> writing lowest energy coordinates.
> 
> Polak-Ribiere Conjugate Gradients converged to machine precision in 147 steps,
> but did not reach the requested Fmax < 1e-05.
> Potential Energy  = -2.41706441033253e+04
> Maximum force     =  1.74065672764869e+00 on atom 875
> Norm of force     =  1.92397357924797e-01
> 
> -------------------------------------
> I was wondering if anyone has any suggestions on how to achieve better
> energy minimization results?  Or identify something that is obviously
> wrong?
> 
Try increasing the precision of PME, pme_order = 6-8 
fourierspacing = 0.1 - 0.08

> Thank you,
> 
> 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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