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 Lemkul

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

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 Lemkul wrote: > > > On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir >> >> I am trying to simulate protein_ligand complex

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

[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