[gmx-users] EnMin & constraints: Hamletic doubt

[Justin Lemkul]

On 6/19/14, 10:05 AM, Nicola Staffolani wrote:
> 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​...
>

Constraining all bonds is common with Gromos96 parameter sets.  I know that 53a6 
was parametrized with all bonds constrained; I am not sure if the full details 
of 43a1 were ever published.  If someone else knows, please chime in.  The 
oldest public reference I know of for Gromos96 is a paper about the software 
suite in general, but not the original parametrization protocol.

>
>>   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... ​
>

The context to which I refer is: what were the goals of the study?  If one wants 
to examine, for instance, vibrational spectra, it would be inappropriate to 
apply constraints (and you'd be forced to use a very small time step).  For 
normal MD investigations, constraints are used to increase the time step for 
better throughput.  My comment about context is also a general one.  People 
often mention previous posts without providing links or looking at the whole 
thread.  There may be very specific reasons for a particular approach, or it may 
turn out that the posted settings were wrong ;)

-Justin

>
>>
>>   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!
>
> Regards,
>
> Nicola​
>
>
>> --
>> ==================================================
>>
>> 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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>
>
>

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

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

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