Dear Sir Thank you very much for your response. Actually, I need dielectric constant = 4 for coulomb force. I have no idea where should I give 4. I thought *epsilon-r: () *will work for me . So If I use epsilon-rf: 4, it will work. am I correct?
On Wed, Aug 16, 2017 at 8:52 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/15/17 9:22 PM, Mohammad Zahidul Hossain Khan wrote: > >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon-r = 4 >> > > epsilon-r is used to change the relative dielectric constant; you > shouldn't do this because it will fundamentally break the electrostatic > convention used by all of the "usual" GROMACS force fields. > > If you're trying to alter reaction field properties, the keyword is > epsilon-rf. See the manual. > > -Justin > > >> On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: >>> >>> Dear Sir >>>> >>>> I am trying to simulate protein_ligand complex using epsilon = 4 and it >>>> is >>>> giving the below error >>>> >>>> >>>> What is epsilon = 4? >>> >>> *2 particles communicated to PME rank 4 are more than 2/3 times the >>> cut-off >>> >>>> out of the domain decomposition cell of their charge group in dimension >>>> x* >>>> >>>> I have no idea how to solve this problem >>>> >>>> >>>> Have you Googled it, or gone to the GROMACS error page, where lots of >>> advice lives? ;) >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> -- >>> 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 > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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. > -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085967165* -- 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.