[gmx-users] Energy minimisation
sudheer.pbm07 at gmail.com
Tue Oct 14 13:57:27 CEST 2008
I am having small doubt on energy minimisation that is
I have started protein system, when I do EM its showing that
Step size too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 800
Double precision normally gives you higher accuracy.
writing lowest energy coordinates,
Steepest Descents converged to machine precision in 45 steps,
but did not reach the requested Fmax < 800.
potential Energy = -1.8373166e+06
Maximum force = 1.5158329e+04 on atom 519
Norm of force = 3.1759754e+04
After this I have reduced my system box size from 7nm to 6.8 cubic box
its showed that "steepest descent converge Fmax<800 in 200 steps".
This is fine.
In second case
I ran minimisation it showed that
"steepest descents didn't converge Fmax < 800"
when I use this output file as input of grompp, for run one more
minimisation it showed "steepest descents converge Fmax < 800".
here I have doubt that why in tha above mentioned two cases first time
didn't converge the minimisation when I do modification like either reducing
box size or doing one more minimization by using the output file of earlier
minimisation then its converging.
Can you give me brief idea why its happening
Thanks in advance
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