On Thu, Jul 18, 2019 at 4:23 AM Gordan Horvat <ghor...@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-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 > >>> > > > >>> > >================================================== > >>> > > > >>> > >-- > >>> > >Gromacs Users mailing list > >>> > > > >>> > >* Please search the archive at > >>> > >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> > >posting! > >>> > > > >>> > >* Can't post? Readhttp://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 togmx-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? Readhttp://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 togmx-users-requ...@gromacs.org. > >> > > > -- ========================================== 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 ========================================== > > > -- > 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. > -- ========================================== 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 ========================================== -- 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.