[gmx-users] [gmx-developers] Fw: Fw: Two questions about PME-User in coulombtype

[Du, Yu]

Berk, thanks for your reply.

I have Cc this email including your answers to the GMX-User.

Regards, 

Yu

> -----Original Messages-----
> From: "Berk Hess" <hess at kth.se>
> Sent Time: 2017-10-18 19:56:30 (Wednesday)
> To: gmx-developers at gromacs.org
> Cc: 
> Subject: Re: [gmx-developers] Fw: [gmx-users] Fw: Two questions about PME-User in coulombtype
> 
> Hi,
> 
> I don't know if I can still mail to the gmx-users list (and I don't have 
> time to check now), so I answer to the devloper list, but please post my 
> answers below to the gmx-users list.
> 
> Cheers,
> 
> Berk
> 
> Answers:
> 
> 1) Correct.
> 2) Correct.
> 3) PME splits the Coulomb interaction into two parts and this splitting 
> depends on beta. All you need to know is that up to the cut-off 
> distance, you exactly get the interaction you set in the table. Beyond 
> the cut-off you get 1/r.
> 
> Your potential values should have 10 decimals to be sure that rounding 
> errors are negligible. In principle, also r should have 10 decimals, but 
> 0.0020000000 is identical to 0.002 (and 0.0000000000 to 0.000 or 0).
> 
> On 2017-10-17 15:15, Du, Yu wrote:
> > Dear GMX Developers,
> >
> > I'm sorry for repeting sending this email to the mail list. I think the PME-User is not common for users to use and the related explanation is scarce.
> >
> > Hope you gurus can help me. Thanks a lot.
> >
> > Yu
> >
> >
> > -----Original Messages-----
> > From: "Du, Yu" <duyu at sioc.ac.cn>
> > Sent Time: 2017-10-15 17:17:14 (Sunday)
> > To: GMX-user <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Subject: [gmx-users] Two questions about PME-User in coulombtype
> >
> > Hi GMX Users,
> >
> >
> > I'm using tabulized potentials between energygrp-table = Protein Ligand. I'm writing to inquiring the details of PME-User parameter.
> >
> >
> > I have seen some discussions in the GMX User mail list and the explanation in user guide. I still can't ensure I have grasped the meaning of PME-User in coulombtype option. The following is my understanding. If anything is wrong please point out. Thanks a lot.
> >
> >
> > 1) Because the mesh part also contributes below the cut-off, the PME mesh contribution is subtracted from the user table by gmx mdrun to get the short-range coulombic interaction below the rcoulomb.
> >
> >
> > 2) The tabulized potential is short-range interaction. If I use coulombtype=User, I only have the short-range interaction defined in the tabulized potetial files and no PME between any components (i.e. Protein, Ligand, SOL, ions) in the system.
> >
> >
> > 3)If I use coulombtype=PME-User instead, I will get the short-range interaction defined in the tabulized potetial files and PME between any components (i.e. Protein, Ligand, SOL, ions) in the system like normal coulombtype=PME.
> >
> >
> > --Next Question--
> > "The PME mesh contribution is subtracted from the user table by gmx mdrun. Because of this subtraction the user tables should contain about 10 decimal places."
> >
> > The second question is how to deal with the PME-User's "10 decimal places" in user guide of the coulombtype option. Does it mean that the original step of r = 0.002 nm in mixed precision should be 0.000000000# nm? What should be the detailed step size of r?
> >
> >
> >
>