[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

Viveca Lindahl vivecalindahl at gmail.com
Fri Apr 6 16:45:48 CEST 2018


There is this ancient gromacs page which I guess you already found:

Here are a couple of references, the second for using virtual sites for
CHARMM lipids:

Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Lindahl, E.
Implementation of the CHARMM force field in GROMACS: Analysis of protein
stability effects from correction maps, virtual interaction sites, and
water models. Journal of Chemical Theory and Computation 6, 459–466 (2010).
Loubet, B., Kopec, W. & Khandelia, H. Accelerating all-atom MD simulations
of lipids using a modified virtual-sites technique. Journal of Chemical
Theory and Computation 10, 5690–5695 (2014).


On Fri, Apr 6, 2018 at 9:51 AM, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hi gmx users,
> I know that it is possible to speed up  the simulations by a factor 2 (by
> using a larger timestep) in GROMACS with virtual interaction sites. By I do
> not find a clear procedure on the web in particular if I use CHARMM. Do you
> have any pointers or procedures and examples of mdp files to share with me
> Thanks
> Stéphane
> --
> 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.

More information about the gromacs.org_gmx-users mailing list