[gmx-users] Umbrella sampling
jalemkul at vt.edu
Sat Nov 25 21:17:04 CET 2017
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.
> 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?
> 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.
> 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
>>>>> 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
>>>> 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 plausibly
>> generate a set of configurations to use.
>> 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
>> Gromacs Users mailing list
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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