[gmx-users] Umbrella sampling

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.

-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 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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-- 
==================================================

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

==================================================