Re: [gmx-users] How can I check external electric field was applied?
Thank you Dan, I used two graphene sheets with freeze and one sodium ion and one chloride ion are between them. It also had same ‘gmx potential’ result when simulated without graphene sheets. I’m now using Gromacs 5.1.4, using PME for Ewald summation with NVE ensemble for this test system. After finishing electric field test, I’m going to use following MDP for my original system. < md.mdp> define = -DPOSRES_GRA -DPOSRES_CNT Coulombtype=PME t_couple = berendsen tc_grps = GRA CNT SOL NA CL tau_t = 0.1 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 300 p_couple = Parrinello-Rahman pcoupletype = semiisotropic tau_p = 0.1 compressibility = 4.5e-5 ref_p = 1.0 constraints = none constraint-algorithm = Lincs E_z = 1 1 0 There is no gmx grompp error with this mdp, I just wonder the applied external e field is 1V. Thank you, Regards :) YK Lee -Original Message- From: "Dan Gil" To: , "이연경" Cc: Sent: 2018. 2. 24 AM 2:36:06 Subject: Re: [gmx-users] How can I check external electric field was applied? Hi, You guessed correctly - gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field. Are you using walls in your system? If so, are you using the 3DC correction along with PME for Ewald summation? If you answered yes to both of these question, you need to use Gromacs version 2016.4 and forwards - there has been an important bug fix. As long as your gmx grompp didn't return any warning or errors, I would expect it to be valid. You can share your MDP file with us and that might help. Dan -- 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.
Re: [gmx-users] How can I check external electric field was applied?
Hi, You guessed correctly - gmx potential only calculates the electric field and potential of the system. It does not take into account the applied field. Are you using walls in your system? If so, are you using the 3DC correction along with PME for Ewald summation? If you answered yes to both of these question, you need to use Gromacs version 2016.4 and forwards - there has been an important bug fix. As long as your gmx grompp didn't return any warning or errors, I would expect it to be valid. You can share your MDP file with us and that might help. Dan On Fri, Feb 23, 2018 at 11:45 AM, 이연경 wrote: > > Dear Gromacs users, > > I’m testing a simple system that has one sodium ion and one chloide ion to > check external electric field. > ( Apply strong field along z axis, so I added the line of E_z = 1 10 0 to > .mdp file. ) > > After a short simulation, I used ‘gmx potential’ to check the field. > > But the result graphs of potential.xvg and field.xvg were different from > my expectation. > > Although I applied 10v/nm along z axis, the electrostatic potential and > electric field was not around 10V. > > Does ‘gmx potential’ calculate electric field and electrostatic potential > including external force I applied, or just a system’s? > > If ‘gmx potential’ does not calculate including external forces, is there > any method to check external field was correctly applied? > > Thanks for your time :) > > YK Lee > > > > -- > 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.
