[gmx-users] How to constrain distance between molecules

[Soren Enemark]

 Dear Gromacs users,
   To what extent is the distance between two molecules constrained?
   My question is because I have run a g_dist to check the distance
   and it was not what I expected. Then I did a test and ran a g_dist before
   and after the mdrun and I found that the distance changes. Why is this??
  Where am I doing something wrong??
   
   I include my md.mdp file and my constraint.ppa file.
   
  md.mdp
  -----------------------
  define                   = -DFLEXIBLE
integrator               = md
dt                       = 0.004
nsteps                   = 5000; 20 ps!
constraints              = all-bonds
nstxout                  = 100
nstvout                  = 100
nstlog                   = 100
nstenergy                = 100
nstxtcout                = 200
energygrps               = Complex_A Complex_B
rlist                    = 1
rcoulomb                 = 1
rvdw                     = 1
  tcoupl                   = Berendsen
tc-grps                  = Complex_A Complex_B SOL_NA+
tau_t                    = 0.004      0.004     0.004
ref_t                    = 300        300       300
  gen_vel                  = no
gen_temp                 = 300
gen_seed                = 173529
   
   
   
  constraint.ppa
  --------------------------------
verbose = yes
runtype = constraint
group_1 = Complex_A
reference_group =  Complex_B
reftype = com_t0
reflag = 1
constraint_direction = 1.0 1.0 1.0
constraint_tolerance = 0.010

   
   Can U plz help me to solve this problem! I also have one question to the
   constraint-direction, if I set this to "0 0 0" then what do I constraint??
   
   Thanks,
   Soren
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060407/9c9aabf5/attachment.html>