[gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

[Abhi Acharya]

Actually, I am really not sure whether diffusion out of the box will affect
the results or not. As long as the system is able to correctly simulate the
intended biological phenomenon i.e. interaction of peptides with membrane,
it is fine. Intuitively, one may say that for a semi-isotropic membrane
system diffusion along XY direction should be fine; but any diffusion along
Z would not be acceptable. Not sure, how this can be correctly handled.

There have been studies like this with other peptides, but none of them
have commented on the above aspect.

On Tue, Sep 27, 2016 at 2:36 PM, Erik Marklund <erik.marklund at kemi.uu.se>
wrote:

> Hi Abhi,
>
> No, restricting the COM motion of the entire system is perfectly fine in
> most cases. From the conservation of momentum, the COM should not change
> its velocity at all. One reason the COM motion needs to be kept at bay
> explicitly is because the accumulation of numerical error during the
> simulation. If you separately remove the COM motion of separate groups you
> will however affect the diffusion of one group relative to the other, for
> example. Is diffusion out of the simulation box really a concern in your
> case?
>
> Erik
>
> > On 27 Sep 2016, at 10:40, Abhi Acharya <abhi117acharya at gmail.com> wrote:
> >
> > Another thing which I don't understand is in case of the peptide group,
> > which I expect to diffuse freely, would COM motion removal be non
> physical?
> > The starting system has 16 peptides added to one side of the membrane.
> Now
> > to allow the peptides to diffuse freely and interact with the membrane, I
> > would assume that translational, rotational and conformational freedom
> > would be required. Wouldn't restricting the COM restrict its dof?
> >
> > Thanks.
> >
> > On Tue, Sep 27, 2016 at 1:59 PM, Abhi Acharya <abhi117acharya at gmail.com>
> > wrote:
> >
> >> What I meant to ask was a way to ensure that the peptides and membrane
> COM
> >> don't drift out of the simulation box, but the peptides should be free
> to
> >> move ( relative to the membrane) within the box. Basically, the best
> way to
> >> simulate the diffusion and subsequent interaction of the peptides with
> the
> >> lipid membrane.
> >>
> >> What I can surmise from previous similar studies is that creating
> separate
> >> comm groups for Membrane, solute and ion and the peptide should be the
> >> correct way. Also, I wanted to know how different nstcomm values would
> >> effect the result especially in the context of complex systems such as
> >> this.
> >>
> >> Just wanted to be sure, before I start the production runs.
> >>
> >>
> >>
> >> On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund <
> erik.marklund at kemi.uu.se>
> >> wrote:
> >>
> >>>
> >>>> On 27 Sep 2016, at 06:26, Abhi Acharya <abhi117acharya at gmail.com>
> >>> wrote:
> >>>>
> >>>> Dear Gromacs users,
> >>>>
> >>>> I am trying to perform a simulations of different concentration of
> >>> peptides
> >>>> in a box with lipid bilayer. In this context, I had a query regarding
> >>> the
> >>>> correct Center-of-Mass removal settings; what would be the correct way
> >>> to
> >>>> ensure that the Membrane is stationary during long simulations while
> the
> >>>> peptides, solutes etc freely diffuse in the box. Based on my
> >>> understanding,
> >>>> I am using the following settings in the parameter file:
> >>>>
> >>>> nstcomm                 = 100
> >>>> comm_mode               = linear
> >>>> comm_grps               = MEMB SOL_ION Peptide
> >>>>
> >>>> Here the Peptide group includes a total of say 16 peptides. Would this
> >>> be
> >>>> the correct way to perform the simulation?
> >>>>
> >>>> Is is possible to set individual nstcomm values for each group so as
> to
> >>>> ensure that the peptides diffuse freely while the membrane stays
> >>> stationary?
> >>>
> >>> Why do you want that in the first place? Membranes aren’t stationary.
> >>>
> >>> Kind regards,
> >>> Erik
> >>>
> >>>>
> >>>> The full mdp settings I intend to use is provided in the following
> link:
> >>>>
> >>>> https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00
> >>> /view?usp=sharing
> >>>>
> >>>> Please advise of what would be the best settings to perform the
> >>> simulation.
> >>>>
> >>>> Best Regards,
> >>>> Abhishek Acharya
> >>>> C-CAMP
> >>>> Bangalore.
> >>>> --
> >>>> 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-request at gromacs.org.
> >>>
> >>> --
> >>> 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-request at gromacs.org.
> >>
> >>
> >>
> > --
> > 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-request at gromacs.org.
>
> --
> 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-request at gromacs.org.
>