[gmx-users] Drude force field

[Justin Lemkul]

On Thu, Jul 18, 2019 at 4:23 AM Gordan Horvat <ghorvat at chem.pmf.hr> wrote:

> I have found this in the NAMD manual:
>
> NAMD has the ability to load GROMACS ASCII topology (.top) and
> coordinate (.gro) files, which allows you to run most GROMACS
> simulations in NAMD.
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node14.html
>
> Is that applicable to the Drude input files prepared by the Gromacs
> Drude distribution?
>

No. To do Drude polarizable simulations in NAMD, you need a CHARMM PSF.

-Justin


> Gordan
>
> --
> Gordan Horvat
> Division of Physical Chemistry
> Department of Chemistry
> Faculty of Science, University of Zagreb
> Croatia
>
> On 18.7.2019. 08:33, gromacs.org_gmx-users-request at maillist.sys.kth.se
> wrote:
> > 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
> >>> > >
> >>> > >==================================================
> >>> > >
> >>> > >--
> >>> > >Gromacs Users mailing list
> >>> > >
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> >>> > >posting!
> >>> > >
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> >>> > >
> >> >--
> >> >Gromacs Users mailing list
> >> >
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> >> >posting!
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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 ==========================================
>
>
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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


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