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?
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-requ...@maillist.sys.kth.se
wrote:
On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi<myun...@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<jalem...@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
> >
> >jalem...@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 jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com ==========================================
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