[gmx-users] eNERGY mINIMIZATION
Mark.Abraham at anu.edu.au
Tue Jan 18 05:25:39 CET 2011
On 18/01/2011 3:12 PM, bharat gupta wrote:
> 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.
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