[gmx-developers] Fw: [gmx-users] Fw: Two questions about PME-User in coulombtype
duyu at sioc.ac.cn
Tue Oct 17 15:35:09 CEST 2017
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.
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.
"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?
More information about the gromacs.org_gmx-developers