[gmx-users] complete energy minimization
Mark.Abraham at anu.edu.au
Wed Mar 19 12:02:35 CET 2008
Justin A. Lemkul wrote:
> Quoting s lal badshah <shahbiochemist at yahoo.com>:
>> Dear experts,
>> Hi! I minimized the system and gies 10,000 nsteps, but the output is:
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy = -1.9742134e+21
>> Maximum force = 4.1648520e+06 on atom 1934
>> Norm of force = 5.6557945e+06
>> What other method I should adopt? or what type of correction I should do ? so
>> that minimization is complete. As before I also did this minimization and
>> then in equilibration it gives faults to me. I read the errors gromacs pages
>> from net but didn't reached to any conclusion. What are the other methods of
>> minimization? Is it creat any problem for me in equilibration?
>> Your guidance will be highly appreciated.
> There is nothing wrong with this minimization output. The process completed and
> left you with a negative potential energy, which is what you're after. What
> might be more useful is a better description of what you are doing and the
> "faults" that you are getting during equilibration.
> What is in your system? What force field are you using? What is in your .mdp
> file? Providing this type of information will help us to help you.
I agree with Justin, except that the magnitude of the PE and forces are
far larger than one would normally see for a few thousand atoms in a
condensed-phase system. This suggests some gross problem. However since
we don't know what the system is, our hands are a bit tied when diagnosing.
More information about the gromacs.org_gmx-users