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? 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. > > > -- > 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.