[gmx-users] Umbrella sampling

[rose rahmani]

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?

>
> 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
>
> ==================================================
>
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