[gmx-users] EnMin & constraints: Hamletic doubt
Nicola Staffolani
nicola.staffolani at gmail.com
Fri Jun 20 14:58:08 CEST 2014
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
"constraints = h-bonds" for the MD (and then so here I can probably safely
enough set Δt = 1 - 2 fs...
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
>>>
>>> ==================================================
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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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