I know the paper but the webpage

Thanks you Viveca 

------------------------------

Message: 2
Date: Fri, 6 Apr 2018 16:45:45 +0200
From: Viveca Lindahl <vivecalind...@gmail.com>
To: gmx-us...@gromacs.org
Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
        <gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
        virtual interaction sites
Message-ID:
        <CABxAduWJh4VDyNpeVu0nzd9dZSx3rVgX=z_4yxnsq04amqm...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

There is this ancient gromacs page which I guess you already found:
http://www.gromacs.org/Documentation/How-tos/Removing_fastest_degrees_of_freedom

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).


--
Viveca


On Fri, Apr 6, 2018 at 9:51 AM, ABEL Stephane <stephane.a...@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
>
> St?phane
>
> --
> 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-requ...@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-requ...@gromacs.org.

Reply via email to