On 1/31/18 12:41 PM, Nick Johans wrote:
Sorry, i think there is sth, maybe i've learnt wrong. let me draw it ;)
| = ZnS SHEET and @=Protein
conf0.gro
|
|
|<------------(Z)distance=1.76----------->@
t=0
|
|
next time if dZ=0.5 so;
|
|
|<---------(Z)distance=1.26-------->@
t=t1
|
|
next time if dZ=0.8 so;
|
|
|<---------(Z)distance=0.96-------->@
t=t2
|
|
I want to tell you this is my last conf.gro
|
|
|
|
|<dist~=0nm>@ t=tn
so WHY it shows me 1.611?how can i proof and calculate this distance?ok
they are not coincident because i have sheet(which interact by it's
surface) and Protein, but why it should be important? because the sheet is
freez and immobile and i just want Z distance. and this distance should be
the absolute distance between 2 point( difference between z=4.287and COM of
protein in each frame). this is all my imagination. What i have
misunderstand?
You're applying a restraint only along z. The protein is free to move in
x and y, and it has done just that. The total COM distance is produced
by gmx distance, but again, the z-component of this vector is in
agreement with what is in pullx.xvg, which is dZ, e.g. the z-component
of the distance. This is the only quantity that matters.
-Justin
best regards
On Wed, Jan 31, 2018 at 8:17 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/31/18 11:22 AM, rose rahmani wrote:
Hi,
This is md_pull.mdp
integrator = md
dt = 0.001
nsteps = 4000000
nstxout = 1000
nstvout = 1000
nstfout = 500
nstlog = 500
nstenergy = 500
nstxtcout = 500
nstlist = 10
rlist = 1.5
coulombtype = pme
rcoulomb = 1.5
vdwtype = Switch
rvdw_switch = 1.0
rvdw = 1.2
pcoupl = no
gen_vel = no
constraints = h-bonds
ns_type = grid
pbc = xy
freezegrps = WAL ZnS
freezedim = Y Y Y Y Y Y
energygrp-excl = WAL WAL ZnS ZnS
energygrps = SOL WAL ZnS Protein NA CL
nwall = 2
wall-atomtype = C C
wall-type = 9-3
wall-density = 150 150
wall-ewald-zfac = 3
ewald-geometry = 3dc
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau-t = 0.1
ref-t = 300
; Pull code
pull = umbrella
pull_ngroups = 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry = distance
pull_dim = N N Y
pull_rate1 = -0.01
pull_k1 = 5000
pull_start = yes
pull_nstxout = 50
-------------------------------------------
pullx.xvg;
@ title "Pull COM"
@ xaxis label "Time (ps)"
@ yaxis label "Position (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 "0 Z"
@ s1 legend "1 dZ"
0.0000 4.287 1.76284
0.0500 4.287 1.75329
0.1000 4.287 1.74622
0.1500 4.287 1.73983
0.2000 4.287 1.73664
0.2500 4.287 1.7377
.
.
3999.7500 4.287 0.258632
3999.8000 4.287 0.258738
3999.8500 4.287 0.258955
3999.9000 4.287 0.260093
3999.9500 4.287 0.25843
4000.0000 4.287 0.258025
-------------------------
Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
whole
Then >>g_dist -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg
this is distwhole.xvg
0.0000000 1.7630774 0.0185155 -0.0197599 -1.7628694
0.5000000 1.7529889 -0.0133090 0.0135729 -1.7528858
1.0000000 1.7453604 -0.0344692 0.0751038 -1.7434030
1.5000000 1.7691813 -0.0621567 0.0087628 -1.7680674
.
.
3997.5000000 1.6120006 0.9964043 -1.2400901 -0.2605782
3998.0000000 1.6122891 0.9971979 -1.2404475 -0.2576084
3998.5000000 1.6124574 0.9966092 -1.2406733 -0.2598433
3999.0000000 1.6115565 0.9968075 -1.2396555 -0.2583475
3999.5000000 1.6120616 0.9964568 -1.2404943 -0.2588253
4000.0000000 1.6116294 0.9952377 -1.2410750 -0.2580390
as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
group (Protein and ZnS sheet) in last frame are too close to each other.
so
why i see 1.611 in distwhole.xvg?
and could you please tell me what is the relevance of pullx.xvg to g_dist
output?as you see pullx.xvg ensure that distance between 2 group is
decreasing, so...?
is there anything i did not consider?
Your output is completely consistent. You're applying a biasing potential
along the z-dimension only, so that's the only distance that mdrun cares
about in establishing the reaction coordinate. The pullx.xvg file contains
the COM coordinate of the "reference" group (group0) and in your case is
just the z-coordinate, so that's the first data column. The second data
column (dZ) is the displacement along the z-axis. Your COM distance results
confirm this - your protein and ZnS are not exactly coincident; they have
different x and y coordinates. But the z column in the distance output
agrees with the pullx.xvg file (when considering the absolute value).
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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