[gmx-users] Umbrella sampling
rose rahmani
rose.rhmn93 at gmail.com
Sat Nov 25 21:59:07 CET 2017
On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/25/17 3:07 PM, rose rahmani wrote:
>
>> Oh sorry this is .mdp file:
>>
>> DEFINE = -DPOSRES
>>
>
> What are you restraining? This seems counterproductive, and by default
>> (unless you've hacked the topology), this is going to restrain your
>> protein, which is definitely wrong.
>
> yes, protein.you mean i should remove it and don't restraint anything? and
> for npt(previous step) run too?
>
>> integrator = md
>> dt = 0.001
>> nsteps = 2000000
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstlog = 500
>> nstenergy = 1000
>> nstxtcout = 1000
>> rlist = 1.5
>> rcoulomb = 1.5
>> rvdw = 1.2
>>
>
> Again, I am suspicious of these cutoffs. What force field are you using?
>
> AMBER99
>
> coulombtype = pme
>> cutoff-scheme = group
>> vdwtype = Switch
>> rvdw_switch = 1.0
>> pcoupl = no
>> gen-vel = yes
>> gen-temp = 0
>> gen-seed = 173529
>> constraints = h-bonds
>> pbc = xy
>> freezegrps = WAL ZnS
>> freezedim = Y Y Y Y Y Y
>> energygrp-excl = WAL WAL ZnO ZnO
>> energygrps = SOL WAL ZnO 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 = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = ZnS
>> pull_group2_name = Protein-H
>>
>
> You can probably just use the whole protein here, though I doubt it makes
> much difference.
>
> pull_coord1_type = umbrella ; harmonic biasing force
>> pull_coord1_geometry = distance ; simple distance increase
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate = 0.001
>>
>
> Here's your problem. With a positive pull rate, you are instructing mdrun
>> to increase the COM distance between the protein and the ZnS surface. If
>> you want them to come closer, you need a negative value here, to decrease
>> the distance as a function of time. Of course, this all goes out the window
>> if your protein is restrained, as suggested above.
>
>
oh, i've got it.
you restrained chain B in tutorial but i shouldn't because ZnS is freezed?
> -Justin
>
>
> pull_coord1_k = 5000 ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes ; define initial COM distance > 0
>>
>>
>> On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 11/25/17 11:49 AM, rose rahmani wrote:
>>>
>>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>>>>
>>>>> I attached md_pull.mdp file
>>>>>
>>>>>> i put " cutoff-scheme = group" beecause of some errors (about energy
>>>>>> groups)
>>>>>>
>>>>>> The use of energygrps has no effect on the physics. You should view
>>>>>>
>>>>> pairwise interactions energies as an analysis method, not something
>>>>> that
>>>>> you need to do as part of your MD run. Don't base your algorithm
>>>>> choices
>>>>> on
>>>>> a quantity that is usually meaningless.
>>>>>
>>>>> This is what i try to do(part of some literatures);
>>>>>
>>>>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>>>>>> surface of ZnO
>>>>>>
>>>>>> 2-Pulling is implemented through a “dummy particle” which moves
>>>>>> towards
>>>>>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>>>>>> and drags the CM by the harmonic force corresponding to the spring
>>>>>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>>>>>> the PMF is averaged laterally
>>>>>>
>>>>>> 3-The conformations are scanned every 0.1 ps in order to save them
>>>>>> with the CM within each of the interval of width 0.05 nm. ( most of
>>>>>> all i'm not sure about this part of my mdp file and i don't know how
>>>>>> should i implement them).
>>>>>>
>>>>>> I don't know what .mdp setting you're referring to here.
>>>>>>
>>>>> Sorry, I didn't understand what you mean?
>>>>>
>>>>> The mailing list does not accept attachments, so your .mdp file did not
>>> come through. I'm working blind on what settings you're using. What I
>>> specifically don't understand here is your connection between the desired
>>> spacing along the reaction coordinate and whatever .mdp settings you
>>> think
>>> affect this. You can only tell mdrun how frequently to save a frame, you
>>> can't tell it anything about the interval along the reaction coordinate
>>> you
>>> care about. Save coordinates frequently enough that you can plausi
>>> <https://maps.google.com/?q=es+frequently+enough+that+you+can+plausi&entry=gmail&source=g>
>>> bly
>>> generate a set of configurations to use.
>>>
>>>
>>> -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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> Gromacs Users mailing list
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