[gmx-users] eNERGY mINIMIZATION

[Mark Abraham]

On 18/01/2011 3:12 PM, bharat gupta wrote:
> Sir,
> That's what  I want to know how u found out that the P.E. is ok and 
> then what about the PE graph ??

A value of large magnitude and negative sign is probably OK. Exactly how 
large varies widely with system composition, force field, etc. So nobody 
worries much about this.

> Does it has to be some what parallel to x-axis in case of every 
> minimized structure as in my case its not parallel to x-axis , rather 
> its getting down towards the x-axis.. ... generally for a miminized 
> structure how it should be ??

Like I said last time, the apparent gradient is not physical, so don't 
stress about it. The physical things are the magnitude of the energy, 
and the magnitude of the force.

> ... I again carried out the minimzation with emtol = 1000 and the 
> values of PE and max force are
>
> Steepest Descents converged to Fmax < 1000 in 826 steps
>
> Potential Energy = -7.1715738e+05
>

OK, so this is a bit lower. Maybe you could go further. Maybe it's 
enough already. That depends on your purpose, but for simulation 
preparation, see my previous email.

> Maximum force = 9.6300812e+02 on atom 1669
>
> Norm of force = 2.0939770e+01
>
> ----------------------
>
> Correct me if I am wrong ... If the Fmax < Emtol , it means that the 
> structure is minimized ??
>

Check out manual section 7.3.5.

> One more thing I want to know .. since we are changing the topol file 
> also while minimzation then the repitition of minimization again would 
> lead to any drastic changes to the topology or not .. as in my case I 
> first did with emtol = 2000 and then with emtol = 1000 ??
>

EM is fast, so you may as well just start from your original structure 
each time, so you have a simple workflow.

Mark