Re: [gmx-users] npt simulation error
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 Lemkulwrote: > > > 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 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 * * 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.
Re: [gmx-users] npt simulation error
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 Lemkulwrote: 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.
Re: [gmx-users] npt simulation error
; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 4 On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkulwrote: > > > 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. > -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: 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.
Re: [gmx-users] npt simulation error
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.
[gmx-users] npt simulation error
Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error *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 -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: 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.