[gmx-users] EnMin & constraints: Hamletic doubt

Nicola Staffolani nicola.staffolani at gmail.com
Fri Jun 20 15:12:21 CEST 2014 

Thank you again for your precious suggestion!!


On 20 June 2014 15:04, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/20/14, 8:58 AM, Nicola Staffolani wrote:
>
>> Sorry, that's true, I am mixing things up! I am using "constraints = none"
>> for EnMin (and here our findings apply → Δt = .5 fs (at least)) & then
>>
>
> dt is irrelevant during energy minimization; only emstep matters since the
> minimization algorithms are not dynamical.
>
>
>  "constraints = h-bonds" for the MD (and then so here I can probably safely
>> enough set Δt = 1 - 2 fs...
>>
>>
> Beware that if you are using constraints in the MD, you should minimize
> with constraints, otherwise the minimized structure may have bond lengths
> that cause the constraint algorithm to fail.
>
> -Justin
>
>
>  Thank you and sorry for being not sufficiently clear!!
>>
>> Nicola
>>
>>
>> On 20 June 2014 14:36, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/20/14, 8:34 AM, Nicola Staffolani wrote:
>>>
>>>  .5 fs even with h-bonds?
>>>>
>>>>
>>>>  No, you can use 1-2 fs with h-bonds, but based on your citation of a
>>> previous post that did not use constraints and then you said:
>>>
>>> "And I was thinking that we should remove the constraints if we want to
>>> see the appropriate oscillations!"
>>>
>>> it sounded like you would not be using constraints.
>>>
>>> -Justin
>>>
>>>
>>>
>>>  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
>>>>>
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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
>>>
>>> ==================================================
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>>> Gromacs Users mailing list
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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