[gmx-users] gmx distance
Nick Johans
johans.nick93 at gmail.com
Wed Jan 31 18:41:20 CET 2018
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?
best regards
On Wed, Jan 31, 2018 at 8:17 PM, Justin Lemkul <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
>
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