[gmx-developers] comb-rule=2 support for forcetable

Du, Yu duyu at sioc.ac.cn
Sun Dec 1 02:41:59 CET 2019

Hi Prof. Hess, 

Thanks for your reply.

It is because user table requires comb-rule=1 that I have to change the comb-rule of AMBER and CHARMM 
from 2 to 1. I realy have no special need for comb-rule!=1. So could you give some hints of "You can 
list parameters for all combinations of atoms types you need/want explicitly."? I don't know the way 
to explicitly list the combined values for all atom pairs.

Yes, I will take your caveat of larger errors.



-----Original Messages-----
From:"Berk Hess" <hess at kth.se>
Sent Time:2019-12-01 02:26:54 (Sunday)
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] comb-rule=2 support for forcetable


But you don't need to change the combination rule. You can list parameters for all combinations of atoms types you need/want explicitly.

Note that changing the combination rule for a force field likely results in much larger errors than the differences between different force fields.



On Nov 30, 2019 14:36, "Du, Yu" <duyu at sioc.ac.cn> wrote:
Hi Prof. Lindahl, 

Thanks for your reply.

If user table is used e.g. coulombtype=PME-user and vdwtype=user, I think that the only difference 
of geometric (comb-rule=1) and arithmetic (comb-rule=2) average of sigma that can't be eliminated 
by editing the value in force field.

comb-rule=1 matches GROMOS force field which is deprecated for its physically incorrect scheme.
comb-rule=2 matches AMBER and CHARMM force fields which I want to use in the a compatible comb-rule
under circumstances of user table.

As you suggested, I indeed have copied and modified AMBER and CHARMM ff with a new name :), but in 
comb-rule=1 for user specified nb potentials between groups. This is why I'm asking for a comb-rule=2

By the way, I notice that forcetable in Verlet scheme has been under development. I'm excited about
it and hope it can move to GPU in the future.


-----Original Messages-----
From:"Erik Lindahl" <erik.lindahl at gmail.com>
Sent Time:2019-11-30 17:08:41 (Saturday)
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] comb-rule=2 support for forcetable

Hi Yu,

That won't really require any changes in the code.

First, the reason we can't "support" it is that force field Lennard-Jones parameters have been determined for a specific set of combination rules and cutoffs, and when you change the combination rules you will change the result of the simulation. How good or bad that is depends on what you are doing, but it's something you'd have to determine and be ready to defend when publishing.

Having said that, if you absolutely want to change the setting for a particular force field, you can just edit the value in the force field file. I would strongly advise making a copy of the entire force field directory and changing its name to reflect this, so you don't forget and have an altered installed version of the force field ruin other simulations later.



On Sat, Nov 30, 2019 at 3:11 AM Du, Yu <duyu at sioc.ac.cn> wrote:

Dear GMX Developers, 

The force table function (src/gromacs/tables/) in GROMACS is a magic, it helps to achieve a lot of work.
Could you please support it in comb-rule=2 for AMBER and CHARMM FF? 

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Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm University
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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