SV: [gmx-users] failing to constraint distance

Fri May 12 18:11:23 CEST 2006

 Hello Gmx-users,
  can it be true that it is not possible to constrain the vector between 2 molecules defined as constrain group and reference group in a ppa file?

 After a longer struggle it seems to me that one can only constrain _one_ of the
 following: I. The length of the vector  II.,III.,IV., The length of the vector onto the x, y, and z, coordinate axis, respectively.

 This means that setting: 
 "constraint_direction = 0.0 1.0 1.0" or 
 "constraint_direction = 1.0 1.0 1.0"

 in the ppa file will constrain _anything_!
 Why is that?

  Best regards
  -Soren

Soren Enemark <blegbirk at yahoo.dk> skrev: Dear Gromacs users,
  I have difficulties to get the distance between two molecules constraint using
  a .ppa file as described in Chapter 6 in the manual. I tried to combine the
  different options in almost all ways but nothing seems to constraint the
  distance.
  To check that the inter molecular distance is unchanged I use g_dist. Is it
  unprecise? Can the inter molecular constraint be used together with the
  normal bond/angle constraints set in the mdp file, or are they somehow
  working against each other?
  I include a test md.mdp file, my constraint.ppa file and a piece of the dist.xvg
  file generated with g_dist

  md.mdp
  -----------------------
  title           = FWS
  integrator      =  md
dt              = 0.001
nsteps          = 2000 ; 2 ps
ns_type         = grid
  pbc             = xyz
nstlist         = 1
rlist           = 1.1
  nstxout         = 10
nstvout         = 10
nstfout         = 10
nstlog          = 10
nstenergy       = 10
nstxtcout       = 0
energygrps      = Complex_A Complex_B
  comm_mode       =  Linear
nstcomm         = 1
comm_grps       = Complex_All
  coulombtype     = PME
optimize_fft    = yes
fourierspacing  = 0.12
pme_order       = 4
rcoulomb        = 1.1
vdwtype         = Switch
rvdw_switch     = 1.1
rvdw            = 1.2
  tcoupl          = berendsen
tc_grps         = Complex_All SOL_NA+
tau_t           = 0.1 0.1
ref_t           = 300 300
  pcoupl          =  berendsen
pcoupltype      = isotropic
tau_p           = 5
compressibility = 4.5e-5
ref_p           = 1.1
  gen_vel         = no
gen_temp        = 300
genseed         = 42
  ;constraints     = hbonds
;constraint_algorithm = lincs
;unconstrained_start = no

  constraint.ppa
  --------------------------------
verbose = yes
runtype = constraint
group_1 = Complex_A
reference_group =  Complex_B
;reftype = com_t0
;reflag = 1
pulldim = Y Y Y
constraint_direction = 1.0 1.0 1.0
;constraint_tolerance = 0.010

    dist.xvg
   --------------------------------

  # This file was created Fri Apr 21 10:37:52 2006
# by the following command:
# g_dist -f traj.trr -s topol.tpr -n index.ndx -o dist.xvg
#
# g_dist is part of G R O M A C S:
#
# God Rules Over Mankind, Animals, Cosmos and Such
#
@    title "Distance"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
   0.000    4.39150    4.39143   -0.00756    0.02317
   0.010    4.39139    4.39132   -0.00756    0.02328
   0.020     4.39129    4.39122   -0.00755    0.02338
   0.030    4.39119    4.39112   -0.00756    0.02349
   0.040    4.39110    4.39103   -0.00759    0.02360
   0.050    4.39102    4.39095   -0.00763    0.02372
   0.060    4.39094    4.39087   -0.00767    0.02384
   0.070    4.39086    4.39079   -0.00770    0.02395
   0.080    4.39079    4.39071   -0.00772    0.02405
   0.090    4.39071    4.39063   -0.00773    0.02414
   0.100     4.39062    4.39054   -0.00774    0.02424
   0.110    4.39052    4.39044   -0.00775    0.02435
   0.120    4.39042    4.39034   -0.00778    0.02448
......

     0.900    4.38858    4.38848   -0.00831    0.02686
   0.910    4.38866    4.38857   -0.00831    0.02677
   0.920    4.38875    4.38866   -0.00830    0.02668
   0.930    4.38883    4.38874   -0.00828    0.02658
   0.940    4.38890    4.38881   -0.00826    0.02649
    0.950    4.38898    4.38889   -0.00824    0.02639
  ......

     1.930    4.39870    4.39867   -0.00592    0.01429
   1.940    4.39872    4.39870   -0.00591    0.01425
   1.950    4.39874    4.39871   -0.00589    0.01422
   1.960    4.39874    4.39871   -0.00586    0.01419
   1.970    4.39874    4.39871   -0.00584    0.01417
   1.980    4.39874    4.39872   -0.00581    0.01413
   1.990    4.39876    4.39874    -0.00577    0.01408
   2.000    4.39880    4.39878   -0.00575    0.01401

  Finding the max and min distance shows that the molecules move 0.1 Ång
  over a period of 1 ps. I am simply demanding too much from the program,
  since each of the molecules are about 450 aa?

  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
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