[gmx-users] protein domain separate

[David van der Spoel]

hazizian wrote:
> Hi
> As I told in my perevious mail, My system consist of a 2-domain protein 
> (Domain A and B), even when I did EM minimization this 2 damain separated.
> 
No they didn't. Check the website.
> my em.mpf is: 
> 
> title               =  n.pdb
> cpp                 =  /lib/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> nsteps              =  40000
> constraint_algorithm  = shake
> shake_tol           = 0.0001
> nstenergy           =  10
> nstxtcout           =  10
> nstlist             =  5
> ns_type             =  grid
> rlist               =  1.2
> coulombtype         =  PME
> rcoulomb            =  1.2
> rvdw                =  1.4
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> 
> ;       Energy minimizing stuff
> ;
> emtol               =  10.0
> emstep              =  0.01
> 
> Also it is not because of pbc, 
> What do you suggest for solving this, thank you very much for replying.  
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se