[gmx-users] minimization

[Nuno R. L. Ferreira]

Your potential energy seems good, so my guess is that minimization went just fine.

That error you are receiving iis just an warnig. No problem at all.
Regards,
Nuno



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Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
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  ----- Original Message ----- 
  From: gold gunaseelan 
  To: spoel at xray.bmc.uu.se ; spoel at gromacs.org 
  Cc: gmx-users at gromacs.org 
  Sent: Monday, April 05, 2004 12:11 PM
  Subject: [gmx-users] minimization


  dear sir ,
  Iam using gromacs 3.2.1
  I changed the following in em.mdp  file as

  define = -DFLEXIBLE and ran energy minimisation but it converged as 

  Stepsize too small, or no change in energy.
  Converged to machine precision,
  but not to the requested precision Fmax < 2000

  Double precision normally gives you higher accuracy.

  writing lowest energy coordinates.

  Steepest Descents converged to machine precision in 202 steps,
  but did not reach the requested Fmax < 2000.
  Potential Energy  = -4.0429609e+05
  Maximum force    =  4.6900386e+03 on atom 1650
  Norm of force    =  1.4885711e+04

  Previously i had given define =-DFLEX_SPC it gave the same error but it converged in 57 steps.I looked in one of ur old reply,in which u have asked to see toplogy file 

  > ; Include water topology
  > #ifdef FLEX_SPC
  > #include "flexspc.itp"
  > #else
  > #include "spc.itp"
  > #endif
  > 
  > then you can try with this file:
  > 
  > 
  > title                    = xxxx
  > cpp                      = /lib/cpp
  > include                  = -I../top
  > define                  = -DFLEX_SPC

  I would like to point out that tis has been changed a bit in 3.2
  If you use spc water this still will work, but for other models the more
  generic way of writing is:

  #include "water.itp" (either tip3p, tip4p, spc, spce)

  define = -DFLEXIBLE

  But i didnot find this in top file

  ; Include water topology
  #include "spc.itp"

  #ifdef POSRES_WATER
  I found these terms missing as specified by u above.
  sir please suggest whats wrong .is protein minimized properly.thanks in advance -gsmith 



   
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