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

Abhi Acharya abhi117acharya at gmail.com
Tue Sep 27 10:29:41 CEST 2016


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.
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