[gmx-users] EM problem for homology model !!
spoel at xray.bmc.uu.se
Thu May 20 13:19:10 CEST 2004
On Thu, 2004-05-20 at 10:57, Kamil Tamiola wrote:
> narender wrote:
> >Dear Users,
> >Hi, i am getting problems in doing energy minimizing of my system of 3400
> >atoms (371 residues). This system is a homology build protein and i want to
> >do atleast 1000 steps of steepest descent. But its converginh to Fmax after
> >just 4 steps . I tried changing emtol and emstep but of no use.
> >Please help !!. Also it would be great if someone could tell me how can i fix
> >my protein's backbone and minimize only the sidechains.
turn off constraints and use l-bfgs for minimizer.
> >thank in advance
> > (My EM input file (.mdp is)
> >cpp = /lib/cpp
> >define = -DPOSRE
> >constraints = all-bonds
> >integrator = steep
> >nsteps = 1000
> >; Energy minimizing stuff
> >emtol = 2300
> >emstep = 0.01
> >nstcomm = 1
> >ns_type = grid
> >rlist = 1
> >rcoulomb = 1.0
> >rvdw = 1.0
> >Tcoupl = no
> >Pcoupl = no
> >gen_vel = no
> >gmx-users mailing list
> >gmx-users at gromacs.org
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> Try to increase the stepsize... for example 0.5 (I had got the same
> problem and it was the solution in my case)
> As for fixing backbone, there is an option "freezegrps" in
> non-equilibirum dynamics, please refer to the manual - version 3.2.1
> page 143.
> Try to minimize the whole structure
> first and than freeze the backbone an run some short MD with velocity
> generation at specified temprature. After this
> extract ener.edr file and investigate the potential and total energy to
> se if there is an equilibrium and when it has equilibrated.
> You can average the structure over given time an be sure that it is in
> local energy equilibirum.
> Good luck,
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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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