[gmx-users] RE: em in normal modes analysis

[David van der Spoel]

On Tue, 2004-09-14 at 13:34, vincenzo venditti wrote:
> Hi all,
> I am trying to energy minimize my protein for a NMA. I've compiled GROMACS 
> in double precision version and I'm using this .mdp file:
> ------------------------------------------------------------------------------------------------------------------------------------------
> title               = 1P67_R2C_E9C
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  cg
> dt                  =  0.002    ; ps !
> nsteps              =  10000
> nstlist             =  10
> ns_type             =  grid
> nstcgsteep           =  100
> rlist               =  0.9
> coulombtype		=  PME
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing		=  0.12
> fourier_nx		=  0
> fourier_ny		=  0
> fourier_nz		=  0
> pme_order		=  6
> ewald_rtol		=  1e-5
> optimize_fft		=  yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  0.001
> emstep              =  0.01
> --------------------------------------------------------------------------------------------------------------------------------------
> 
> Nevertheless in the .log file I find :
> 
> Polak-Ribiere Conjugate Gradients converged to machine precision in 187 
> steps,
> but did not reach the requested Fmax < 0.001.
> Potential Energy  = -3.47556312352537e+04
> Maximum force     =  8.04322685559554e+00 on atom 250
> Norm of force     =  4.12079516782199e-01
> 
> What can I do to improve my energy minimization?
integrator = l-bfgs
if it is not in solvent you may want to run without PBC and cut=offs
> 
> Thanks,
> Vincenzo
> 
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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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