[gmx-users] monoclinic systems and pbc

Claus Valka lastexile7gr at yahoo.de
Tue Dec 12 20:29:08 CET 2006

 Title : monoclinic polymeric crystal 12/12/06
 I 'm trying to simulate a polymeric crystal in
 I face some problems and I would appreciate your
 Sorry for the lengthy email, I am trying to be
 since I realized that I couldn't find much info about
 the use of monoclinic systems within gromacs.
 The unit cell is monoclinic with the following
parameters :
 i) unit cell vectors (in nm)
 a = 0.663   (corresponds to x)
 b = 2.078   (corresponds to y)
 c = 0.665   (inclined vector)
 ii) unit cell angles
 b^c = 90   (angle between b and c vector)
 a^c = 99,5
 a^b = 90
 In my specific situation I use 4 unit cells in every
direction so all the 
 numbers above are multiplied by 4. The number of
chains in the unit cell
 is 4, the chains are parallel to the inclined axis of
the monoclinic system, 
 so, from the repetition of the unit cell in the x-y
 there are in total 4x4x4=64 chains in the used
 In the gro file I insert the cartesian coordinates of
the monoclinic supercell,
 and also the cartesian coordinates of the atoms in
the same system.
 For the monoclinic axes I enter
 ax = 4*0.663, by = 4*2.078,          cz =
 ay = 0,       az = 0,                bx = 0, 
 bz = 0,       cx = 4*0.665*cos(a^c), cy = 0
 Question 1: Am I passing correctly my system to
gromacs, or should I use directly the monoclinic 
 coordinates (I guess no)? 
 I have found out from the gromacs community
 that the pbc in the mdp file in the case of a crystal
should be better put as pbc=full.
 Question 2: What is the difference between pbc=full
and pbc=xyz. 
 With pbc=xyz and energy minimization grompp gives the
following from md.log:
      Removing pbc first time
      There were 64 inconsistent shifts. Check your
      Done rmpbc
      Steepest Descents:
      Tolerance (Fmax)   =  1.00000e+02
      Number of steps    =         1000
      There were 64 inconsistent shifts. Check your
  The output gro file preserves the form of the
monoclinic system (something that might be 
  against the philosophy of gromacs since it is stated
in the manual that the simulation 
  is held in a brick shaped box).
  With pbc=full and energy minimization the output is
a cubic box. 
  With the command, 
       trjconv -f .gro -pbc whole -ur tric -o
  I can see again a monoclinic system, yet shorter in
the direction of the inclined axis,
  i.e., the initial chains have been folded inside the
shorter monoclinic cell. They also
  seem to be cut in one point and once again I see the
message of the 64 inconsistent shifts. That is,
  I do not recover the original input supercell.
  Question 3: Both with pbc=(xyz | full) I face
problems, i.e., 
  (inconsistent shifts | cannot recover original cell,
broken chains).
  Is it sth wrong in the way I load my system to
gromacs, or should I check my topology file
  for errors, which I have not yet managed to locate. 
  Question 4: Should I stick with pbc=full?
              What is the meaning of inconcistent
  Question 5: Should I change the way I use trjconv?
              I guess that with the use of trjconv,
from the output cubic cell of gromacs
              I should be able to recover the initial
monoclinic supercell.
  Thank you very much,

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