[gmx-users] EnMin & constraints: Hamletic doubt

[Nicola Staffolani]

.5 fs even with h-bonds?


On 20 June 2014 14:29, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/20/14, 4:01 AM, Nicola Staffolani wrote:
>
>> On 19 June 2014 23:59, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> 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
>>> ;)
>>>
>>>
>>>  ​Thanks for explaining! Indeed we are in a early phase of our study and
>> are
>> interested in the vibrational (Raman) spectra (!!) of Cu-ligands; we want
>> to see whether we are able to reproduce the experimental spectra in order
>> to validate our model and then go further... And I was thinking that we
>> should remove the constraints if we want to see the appropriate
>> oscillations!
>>
>> It is also very interesting your comment about the relation between time
>> step duration and aim of the MD simulation: I had been suggested to use Δt
>> = 0.002 ps, but then I had issues with the frozen Au layers and changed it
>> to 0.001 ps. Afterwards, in my last runs, I changed some other parameters
>> and decided to give a try again to 0.002 ps, but it seems more appropriate
>> - thanks to your comment - to switch back to 0.001 ps...
>>
>>
> Without constraints, you may need an even smaller time step, 0.5 fs at
> most, for proper energy conservation.
>
> -Justin
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
"New ideas, fragile as spring flowers, easily bruised by the tread of the
multitude, may yet be cherished by the solitary wanderer.", Fred Hoyle, *The
Black Cloud*.

"Everybody knows that something can't be done until somebody turns up who
doesn't know that it can't be done and he does it.", Albert Einstein

Sometime ago I met a fellow who was wearing an abnormally long tie - I
mean, it was abnormally long because of how the knot had been made, not
because the tie was an abnormally long one, and so I asked him why such an
abnormally long tie, and you know what he told me? That the tie belonged to
his grandfather!!