[gmx-users] Umbrella sampling

[Justin Lemkul]

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.

> 4-between 36-38 conformations should be collected and i dont know how
> should i choose them between 710 conf.gro files( i got 710
> conformations after using trajconv)

Calculate the COM distance between the groups for each frame. This is 
what my tutorial does and what my provided scripts help you to analyze. 
Compile a list of the COM distances and determine which frames are 
suitable for starting points of each window.

-Justin

> this is first part of my job.
>
> protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.
>
> what do you think about mdp file? where did i make a mistake?
>
> Thank you for your attentions (like always ;) )
>
> Best Regards
>
>
>
>
>
> Sent from my iPhone
>
>> On Nov 24, 2017, at 19:34, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> On 11/24/17 9:14 AM, Rose wrote:
>>> Hello
>>>
>>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling.
>>> To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as I'm not good in programming I couldn't understand what happened there?!
>> Run gmx distance manually. It's probably returning some error, so the script fails. I've heard this reported a number of times and no one's ever told me what the solution is, so unfortunately there's nothing I can do to fix it.
>>
>>> How did you know for example:
>>> 50>>>0.6 nm
>>> 100>>>0.8 nm
>> This is what gmx distance computes.
>>
>>> I need deltaz=0.05nm
>> Then you will need to save frames very frequently. This is a very narrow dz, and may be overkill depending on what the system is.
>>
>>> Please help me, i don't know where should i find these informations and modify them.
>>>
>>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and
>> What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs used by any given force field, as you will get unexpected (or invalid) results...
>>
>>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab.
>>> What is my mistake?!
>> You'll have to provide an .mdp file and a complete description of your system, how you constructed it, and what your objectives are. Images would help.
>>
>> -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

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