[gmx-users] problem regarding energy minimization

[Mark Abraham]

sangeeta kundu wrote:
> Dear Sir,
> 
>  
> 
>             I want to minimize an average structure obtained from a 
> simulation, by conjugate gradient method.. As this method is more 
> efficient than steepest descent I am trying with this method. The 
> minimization has gone smoothly with steepest descent and lbfgs, but it 
> failed while using conjugate gradient giving the following error message.
> 
>  
> 
>  
> 
> processing coordinates...
> 
> double-checking input for internal consistency...
> 
> ERROR: can not do Conjugate Gradients with constraints (8901)
> 
> -------------------------------------------------------
> 
> Program grompp, VERSION 3.3.1
> 
> Source code file: grompp.c, line: 1109
> 
>  
> 
> Fatal error:
> 
> There were 1 error(s) processing your input
> 
>  
> 
> I used Dflexible water model and there was no constraints in my mdp 
> file. My question is
> 
>  
> 
>  1) Which method is better to minimize an average structure?  
> 
> 2)  What is happening here, I can not detect the error.

See 
http://wiki.gromacs.org/index.php/Energy_Minimisation#Conjugate_gradient_minimization_and_constraints

Your topology must be defining some constraints, either through actually 
using a non-flexible water molecule, being overridden by the .mdp file 
flags, or explicitly defined in the .top or .itp files. In particular, 
in the .mdp file "-Dflexible" will not have the same effect as "-DFLEXIBLE".

Mark