[gmx-users] minimization problem

[David van der Spoel]

Hongyan Xiao wrote:
> Hi, David van der Spoel 
>  
> I used the periodic boundary conditions. The box 
> is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is 
> the em.mdp file.

Then the minimization works correctly. See chapter 3 in the manual.

>  
> ;
> ;       User xiao
> ;       2008.9.28 10:23
> ;       Input file
> ;
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> nsteps              =  20000
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  0.8
> coulombtype         =  cut-off
> rcoulomb            =  1.2
> vdwtype             =  cut-off
> rvdw                =  1.2
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> Please help me. Thanks again!
>  
> H. Y. Xiao
>  
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
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