[gmx-users] Position restraints : POSRES field

[Nuno R. L. Ferreira]

Hi again

Took a look at the outputs from cpeptide MD run in the gmxdemo
(/share/tutor).
Here's some of pieces of it:


output.pdb2gmx
------------------
.....
Reading cpeptide.pdb...
Read 108 atoms
Analyzing pdb file
There are 1 chains and 0 blocks of water and 13 residues with 108 atoms

  chain  #res #atoms
  1 ' '    13    108
........

So, there is 108 heavy atoms --> pores.itp with 108 lines

output.grompp_pr
------------------
....
processing topology...
turning all bonds into constraints...
turning all bonds into constraints...
#     ANGLES:   836
#      PDIHS:   370
#      IDIHS:   350
#       LJ14:   738
#     POSRES:   216
#     CONSTR:   432
#     SETTLE:   976

The same thing appened to me .
POSRES: 2*(atoms to position restraint).

Sugestions.
Nuno

#######
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal

Phone: +351 239 852080
Fax: +351 239 827703
www.biolchem.qui.uc.pt
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