[gmx-users] Simulated annealing

Xavier Periole periole at inka.mssm.edu
Wed Jul 30 21:36:04 CEST 2003

  1- editconf -f p.gro -o p.gro -bt cubic -c -d 0.7
  2- genbox -cp p.gro -cs spc216.gro -o p.gro -p p.top
  my peptides have diferent structure , and then my BOX 
  and my number of H2O are diferent, my question is
  hOW COULD I GENERATE  exactly the same number of solvent 
  molecules and box size.

include the solvent in your SA. I did that too with gromacs. It works
fine. And don't need a big box for 11 residues. 

The implicit solvent SA I used before was with CHARMM implemented
in the lab by. S. Hassan. Can write him a message at
mago at inka.mssm.edu you'll need CHARMM though

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