[gmx-users] Drude force field

[Justin Lemkul]

On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi <myunggi at pukyong.ac.kr> wrote:

> Thank you Dr. Lemkel,
>
> I don't have ions in my simulation. It's a neutral system with a protein in
> membrane bilayer with solvent.
> I have downloaded the force field (Drude FF for charmm FF in Gromacs
> format). to run the simulation with charmm FF in "Gromacs 2019.3".
> However, it seems the format of the file does not match with the current
> version.
>
> In the web,
>
> Compile and install as you would any other (post-5.0) GROMACS version. If
> you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will
> not be accessible.*
>
> There are 5.0 and 5.1 series of Gromacs versions. Which one should I use?
>
> Or, it there a way to modify the force field format to use the current
> version of Gromacs?, Then I will modify the format.
>
>
Read the information at the previous link more carefully. You cannot use
any released version of GROMACS. You must use the developmental version as
instructed in that link.

-Justin


>
> On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > > Dear users,
> > >
> > > I want to run a simulation with a polarizable force field.
> > >
> > > How and where can I get Drude force field for the current version of
> > > Gromacs?
> >
> > Everything you need to know:
> >
> > http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> >
> > The implementation is not complete. If your system has ions, do not use
> > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> > OpenMM. The Drude model is still considered experimental, hence it is
> > not officially supported yet. There have been a lot of snags along the
> > way (mostly in my time to get the code up to par for official inclusion).
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
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-- 

==========================================

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com


==========================================