[gmx-users] Problem with Na

[David]

On Fri, 2003-12-05 at 19:04, Mauricio Arenas Salinas wrote:
> hi All:
> i try to do MD for protein with Na and water,  but when 
> the EM finishes, the final structure does not 
> present/display moleculas of Na. To that can have this? 

are they in the confout.gro file?

what do you mean display?

> and q I can make to solve it?
>   topology:
> 
> Include forcefield parameters
> #include "ffgmx2.itp"
> 
> ; Include chain topologies
> #include "cysk_A.itp"
> #include "cysk_B.itp"
> #include "ions.itp"
> 
> ; Include water topology
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
> 
> [ system ]
> ; Name
> Protein in water
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> SOL             23792
> Na                 12
> 
> 
> Thank you very much
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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