# [gmx-users] SD and EM

Luciano ltcosta at universiabrasil.net
Thu Nov 20 19:11:01 CET 2003

Hi gmx-users and specially David and Anton very very thanks for advise.

I have been read the last mails about EM (SD and CG) and doing EM to my
system (
protein + water) without pbc it have showed to emtol = 10000:

Tolerance         =  1.00000e+04
Number of steps   =         1000
F-Norm            =  1.21548e+05

Step 1, E-Pot = 7.2018726562e+04, Fmax =  8.01764e+03, atom = 1155

writing lowest energy coordinates.

Back Off! I just backed up octa20orig.trr to ./#octa20orig.trr.15#

Back Off! I just backed up after_em_pr.gro to ./#after_em_pr.gro.15#

But when I set emtol = 7000 to next step the result was:

Conjugate Gradients converged to 10000 in 2 steps
Potential Energy  =  7.20187e+04
Maximum force:  8.01764e+03

Negative w:  -5.389869190490e+21
z=  -2.909245276160e+11
gpa=   3.167263553258e+11, gpb=   2.842420549736e+11
a=   0.000000000000e+00, b=   1.130758611745e-10
EpotA=   7.016328906250e+04, EpotB=   7.019690625000e+04
Negative number for sqrt encountered (-5389869190490223542272.000000)
Terminating minimization

writing lowest energy coordinates.

Back Off! I just backed up octa20orig.trr to ./#octa20orig.trr.16#

Back Off! I just backed up after_em_pr.gro to ./#after_em_pr.gro.16#

Conjugate Gradients did not converge in 3 steps
Potential Energy  =  7.01633e+04
Maximum force:  3.67083e+05
What are the terms z, gpa, gpb, a and b? Why the negative number for sqrt?!
What I should do?! About the message of Martina Bert, Sun, 16 Nov 2003
01:53:35 -0600, what the matter when the message comes up?

"Stepsize too small (... nm) Converged to machine precision"

Luciano

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Luciano Tavares da Costa
Mestre em Engenharia Química
icq #232852036 ; ltcosta at universiabrasil.net
Doutorando Laboratório de Biofisicoquímica
Instituto de Química - USP

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------------------------------------------------------------------------
Vote no Universia para o Prêmio IBest 2004 e concorra a uma
viagem para Trancoso.
www.universiabrasil.net

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