[gmx-users] EM problem for homology model !!

[David]

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
> >NSM
> >
> >
> > (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
> >~
> >~
> >~
> >~
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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,
> 
> Kamil
> 
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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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