[gmx-users] Artifact in pull-pbc-ref-prev-step-com
Alex
alexanderwien2k at gmail.com
Fri Apr 24 20:33:14 CEST 2020
Hi Magnus,
I see, many thanks for the insights.
On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg <
magnus.lundborg at scilifelab.se> wrote:
> Hi Alex,
>
> pull-group1-pbcatom lets you specify the exact atom used as the PBC
> reference. Both 0 and -1 are special cases. For small molecules 0 is
> (almost?) always OK. Find one in the center of you membrane (in the pull
> direction). I'll actually have to check if -1 is even compatible with
> pull-pbc-ref-prev-step-com. It's possible that that combination should
> not be allowed even.
>
So, the pull-group1-pbcatm could be any other number as atom number rather
than 0 and -1.
>
> As you say, you can define a subgroup within the larger membrane group,
> but that is mainly of use if you know that some atoms consistently in
> the center of the whole group and others are more flexible.
>
In this case where the subgroup defined in index.ndx file has more than one
atom e.g. 30 atoms, which one of the atom in subgroup should be assigned to
the pull-group1-pbcatom?
If I am not mistaken, here, the entry number in index.ndx file belong to
the subgroup should be assigned to the pull-group1-pbcatom.
[ system ]
[ Other ]
....
[ non-water ]
[ subgroup ]
Would you please confirm if I am correct?
Thank you
Alex
> Regards,
>
> Magnus
>
> On 2020-04-21 16:24, Alex wrote:
> > Hi Magnus,
> > Actually I am confused with the available options for the
> > "pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom".
> > For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when
> > one of the group is large, even the 2020.1 version of grmacs would give a
> > warning if one used No in a case of presence of a large group.
> > Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0
> > the middle atom (number wise) of the large group is used automatically
> > which is safe only for small groups as manual states. So, only
> > remaining option is -1.
> > So, what I understood for a layered-large group similar to what I have
> one
> > should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1
> > which would cause moving the system along -Z during the pulling.
> >
> > Using gmx select, can I manually define a sub-group around the COM of the
> > large group, and consider it as one of the pulling groups instead of the
> > large group?
> >
> > Thank you
> > Alex
> >
> > On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg <
> > magnus.lundborg at scilifelab.se> wrote:
> >
> >> Hi Alex,
> >>
> >> I don't see why it would need pull-group1-pbcatom = -1. Why not pick a
> >> central atom?
> >>
> >> Regards,
> >>
> >> Magnus
> >>
> >> On 2020-04-20 13:40, Alex wrote:
> >>> Hi Magnus,
> >>> Thanks.
> >>> The problem raises only because of using the pull-pbc-ref-prev-step-com
> >>> which needs the pull-group1-pbcatom to be -1 to be meaningful.
> >>> For an identical system and mdp parameters using 2018 version of
> gromacs
> >>> which is independent to the pull-pbc-ref-prev-step-com, I see no issue.
> >>>
> >>> Regards,
> >>> Alex
> >>>
> >>> On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg <
> >>> magnus.lundborg at scilifelab.se> wrote:
> >>>
> >>>> Sorry, about the statement about pbcatom -1. I was thinking about 0. I
> >>>> don't know if pbcatom -1 is good or not in this case.
> >>>>
> >>>> Regards,
> >>>>
> >>>> Magnus
> >>>>
> >>>> On 2020-04-20 09:24, Magnus Lundborg wrote:
> >>>>> Hi Alex,
> >>>>>
> >>>>> I don't think this is related to using pull-pbc-ref-prev-step-com.
> >>>>> Have you tried without it? However, it is risky using pbcatom -1,
> >>>>> since you don't know what atom you are using as the initial
> reference.
> >>>>> I would suggest picking an atom you know is located at the centre of
> >>>>> the structure.
> >>>>>
> >>>>> I would think that the problem has to do with the comm removal. What
> >>>>> are your parameters for comm-mode, nstcomm and comm-grps? It is
> >>>>> possible that you need to lower your nstcomm. It is also possible,
> but
> >>>>> not certain, the comm-mode Linear-acceleration-correction might help
> >>>>> you. For some reason, it seems like I have sometimes avoided similar
> >>>>> problems by using the sd integrator instead, but I haven't evaluated
> >>>>> that properly - it might just have been coincidences. If you see a
> >>>>> clear difference using the sd integrator it might be good if you'd
> >>>>> file an issue about it on gitlab so that someone can look into if
> >>>>> there is something wrong.
> >>>>>
> >>>>> Regards,
> >>>>> Magnus
> >>>>>
> >>>>> On 2020-04-18 20:12, Alex wrote:
> >>>>>> Dear all,
> >>>>>> To generate the initial configurations for umbrella sampling, I
> >>>>>> conducted a
> >>>>>> simple pulling simulation by which a single-small molecule (mol_A)
> is
> >>>>>> being
> >>>>>> dragged along -Z from water into the body of a thin film.
> >>>>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com =
> >>>>>> yes" and
> >>>>>> "pull-group1-pbcatom = -1"* which cause a net shifting of the
> >>>>>> system
> >>>>>> along the pulling direction as soon as the mol_A reach to the thin
> >> film,
> >>>>>> please find below the pulling flags movie and plot in below links.
> >>>>>>
> >>>>>> Centering the thin film and mol_A could solve the issue, (echo 1 0
> |
> >>>>>> trjconv -center yes) to some extent but still COM changes in the
> early
> >>>>>> stage below 2ns. ,
> >>>>>> COM:
> >>>>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0
> >>>>>>
> >>>>>> Movie in which the water molecules are hidden:
> >>>>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv
> >>>>>>
> >>>>>> -
> >>>>>> gmx version 2020.1
> >>>>>> -----
> >>>>>> pull = yes
> >>>>>> pull-print-com = no
> >>>>>> pull-print-ref-value = yes
> >>>>>> pull-print-components = Yes
> >>>>>> pull-nstxout = 1000
> >>>>>> pull-nstfout = 1000
> >>>>>> pull-pbc-ref-prev-step-com = yes
> >>>>>> pull-ngroups = 2
> >>>>>> pull-ncoords = 1
> >>>>>> pull-group1-name = Thin-film
> >>>>>> pull-group1-pbcatom = -1
> >>>>>> pull-group2-name = mol_A
> >>>>>> pull-group2-pbcatom = 0
> >>>>>> pull-coord1-type = umbrella
> >>>>>> pull-coord1-geometry = direction
> >>>>>> pull-coord1-groups = 1 2
> >>>>>> pull-coord1-dim = N N Y
> >>>>>> pull-coord1-origin = 0.0 0.0 0.0
> >>>>>> pull-coord1-vec = 0.0 0.0 -1.0
> >>>>>> pull-coord1-start = yes
> >>>>>> pull-coord1-init = 0
> >>>>>> pull-coord1-rate = 0.0005
> >>>>>> pull-coord1-k = 5000
> >>>>>> -----
> >>>>>> I wonder if I could extract correct initial configuration from this
> >>>>>> trajectory? With correct initial configuration, I mean a set of gro
> >>>>>> file in
> >>>>>> which change from one from to another is the distance between the
> COM
> >> of
> >>>>>> the thin-film and mol_A?
> >>>>>>
> >>>>>> Thank you
> >>>>>> Alex
> >>>> --
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