[gmx-users] Umbrella sampling

Justin Lemkul jalemkul at vt.edu
Sat Nov 25 20:56:24 CET 2017

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 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


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