[gmx-users] Energy Minimization problem

[Venky Krishna]

Hi George,

I usually delete/move the molecules reported to have high force  
values in the minimization steps. A better thing would be to start  
with a box which has sufficient intermolecular distance again by  
deleting molecules which are very close to each other (use the  
g_mindist program) and then energy minimize the system. Btw...did you  
define FLEXIBLE for water molecules during your em runs?

Best
Venky

On Apr 18, 2007, at 5:24 PM, George Abadir wrote:

> Hi,
>      I am doing an energy minimization for a carbon nanotube (end  
> capped with hydrogen atoms) in a box of water. I get the following  
> message:
> " Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision  Fmax < 10
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn off  
> constraints altogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 1836 steps, but  
> did not reach the requested Fmax < 10.
> Potential Energy = -2.4277438+06
> Maximum force = 5.9858018+03  on atom 13
> Norm of force =  5.1364398+04"
>
> The potential energy is extremely low and the maximum force is  
> considerably large. I turned off the constrained and tried other  
> energy minimization methods but still got the same error (with  
> different magnitudes of the force and energy of course). Is it  
> likely that double precision simulation can make such a big  
> difference? If not (which I think) is there any other way to solve  
> the problem?
>
> Thank you very much in advance,
> George Abadir
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