[gmx-users] Drude force field

[Gordan Horvat]

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-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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>>> > >
>> >--
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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 ==========================================