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
dt = 0.001
nsteps = 2000 ; 2 ps
ns_type = grid
pbc = xyz
nstlist = 1
rlist = 1.1
nstlist = 1
rlist = 1.1
nstxout = 10
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy = 10
nstxtcout = 0
energygrps = Complex_A Complex_B
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy = 10
nstxtcout = 0
energygrps = Complex_A Complex_B
comm_mode =
Linear
nstcomm = 1
comm_grps = Complex_All
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
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
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
pcoupltype = isotropic
tau_p = 5
compressibility = 4.5e-5
ref_p = 1.1
gen_vel = no
gen_temp = 300
genseed = 42
gen_temp = 300
genseed = 42
;constraints = hbonds
;constraint_algorithm = lincs
;unconstrained_start = no
;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
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
......
# 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
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
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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