[gmx-users] EnMin & constraints: Hamletic doubt

Nicola Staffolani nicola.staffolani at gmail.com
Thu Jun 19 16:05:51 CEST 2014

Dear Justin,

thank u 4 replying!

On 19 June 2014 15:04, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 6/19/14, 4:11 AM, Nicola Staffolani wrote:
>> Dear GMX community,
>> ​I am running simulations of a solvated protein on a (frozen) Au
>> substrate,
>> but I think that my question is so basic that it falls outside the details
>> of my case...
>> So, the question is: when I prepare the system by minimizing the energy,
>> should I set constraints = all_bonds, h_bonds or none?
> What was your force field parametrized to use?  Most commonly, modern
> force fields constrain bonds involving H, though all bonds are frequently
> constrained in practice because the differences are generally small and the
> rigid representation of a bond is considered by many to be a more realistic
> representation of the ground state than a harmonic function.
> I do not understand your question... ​Do you mean which force field I am
using? In this case the answer is gromos43a1​...

>  IMHP, I should set it to all_bonds, otherwise I may risk that the system's
>> energy minimum corresponds to a configuration very different from the
>> initial one... However, I saw  somebody is using constraints = none and I
>> was wandering why...
> Without context, answering that is impossible.
> ​I see... How can I better describe the context ? Which info do u need? ​
​I have seen setting the constraints to none with the same very system as
mines (solvated azurin on Au​
​ layers) where the ff used was again gromos43a1... ​

>  Would somebody take the pleasure to embark on the discussion of such an
>> issue with me? Thnx in advance,
> There ha
> ​​
> ve been numerous discussions on the underlying theory of constraints and
> their proper application; a bit of searching should turn them up.  Several
> have occurred very recently on this very list.
> -Justin
> ​Thank you very much again for answering!



> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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