[gmx-users] Insertion of Ion-channels onto the membrane using g_membed with Amber force field

[Mark Abraham]

Hi,

I'd start by considering the options at
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation

Mark

On Wed, Dec 6, 2017, 6:12 PM Dhaniram Mahato <bioinfojsr at gmail.com> wrote:

> Thanks for the reply.
>
> For all-atom Amber ff, Should I change the neighbor list value or change in
> the cut-off for VdW interactions. As the side-chain hydrogen atoms might be
> clashing with the lipid atoms and thus producing many LINCS warning.
>
> Thanks
> Ram
> --
> 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.
>