Berk, thanks for your reply. I have Cc this email including your answers to the GMX-User.
Regards, Yu > -----Original Messages----- > From: "Berk Hess" <h...@kth.se> > Sent Time: 2017-10-18 19:56:30 (Wednesday) > To: gmx-develop...@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" <d...@sioc.ac.cn> > > Sent Time: 2017-10-15 17:17:14 (Sunday) > > To: GMX-user <gromacs.org_gmx-users@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? > > > > > > > -- 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.