[gmx-users] Umbrella sampling

[rose rahmani]

Oh sorry this is .mdp file:

DEFINE                   = -DPOSRES
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
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
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
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 plausibly
> 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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