Thank you again for your precious suggestion!!
On 20 June 2014 15:04, Justin Lemkul <jalem...@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 <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. >>> >>> >> >> >> > -- > ================================================== > > 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*. "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!! -- 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.