[gmx-users] gmx distance
Justin Lemkul
jalemkul at vt.edu
Wed Jan 31 18:44:21 CET 2018
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 <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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--
==================================================
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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