[gmx-users] Steepest Descents converged to machine precision

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 27 12:42:47 CEST 2009

nitu sharma wrote:
> Dear mark
> But how can it possible that starting structure is grossly broken , up 
> to infltegro first step I enquired my structure It looks fine but after 
> doing enegy minimisation step i saw that structure is disturbed

OK so what can you deduce from that? It was fine, and then some forces 
acted on it...

> May be its due to restrain not working on protein . To apply position 

So simplify your problem - don't use the restraints, and see what happens.

> restrain on protein I have edited posre.itp file with force constant 
> 100000 and included it in topology file-
>  Include forcefield parameters
> #include "ffG53a6_lipid.itp"
> #include "topol_A.itp"
> #ifdef POSRES
> #include "posre_A.itp
> #include "topol_B.itp
> #ifdef POSRES
> #include "posre_B.itp
> #endif
> But its not working .
> I am unable to understand why?

The above is nonsense. You haven't matched #ifdef with #endif, or 
opening with closing quotation marks.


More information about the gromacs.org_gmx-users mailing list