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 <jalem...@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 <jalem...@vt.edu> wrote: >> >> >>> >>> On 6/20/14, 4:01 AM, Nicola Staffolani wrote: >>> >>> On 19 June 2014 23:59, Justin Lemkul <jalem...@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 <jalem...@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 >>> >>> jalem...@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-requ...@gromacs.org. >>> >>> >> >> >> > -- > ================================================== > > 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 > > jalem...@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-requ...@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*. 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