[gmx-users] Using lennard jones and buckingham terms simultaneously
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Mar 30 21:02:05 CEST 2010
On 31/03/2010 1:40 AM, Gareth Tribello wrote:
> Hello again
>
> Still trying to get this carbonate forcefield to work with gromacs. I
> now know that the tables and so on are being read in correctly as I can
> get gromacs to reproduce the energies that I get for the various terms
> when I calculate them by hand/with a separate program. There is stilla
> a problem with the charge groups however. As when I attempt to split up
> the atoms in the water molecule the simulation fails. Again checking
> that I am doing this correctly I would replace:
>
> ; at type res nr res name at name cg nr
> charge mass
> 1 amber99_61 1 SOL OW 1 0
> 16.00000
> 2 amber99_60 1 SOL HW2 1 0.52422
> 1.00800
> 3 amber99_60 1 SOL HW3 1 0.52422
> 1.00800
> 4 MW 1 SOL MW4 1
> -1.04844 0.00000
>
> with
>
> ; at type res nr res name at name cg nr
> charge mass
> 1 amber99_61 1 SOL OW 1 0
> 16.00000
> 2 amber99_60 1 SOL HW2 2 0.52422
> 1.00800
> 3 amber99_60 1 SOL HW3 3 0.52422
> 1.00800
> 4 MW 1 SOL MW4 4
> -1.04844 0.00000
>
> The problem I get (even if I just run water without any
> carbonate/tabulated potentials) if I do the above is that the settles
> algorithm fails.
I'm surprised GROMACS even tries SETTLE with your modified water charge
groups. Anyway, you can turn it off and try again and report back. You
would have to think very carefully how any optimized water model
interacts with your (probably) fundamentally broken model of physics.
> I'm obviously missing something fundamental - I'm not even sure that cg
> nr stands for the charge group. Any help would be greatly appreciated.
"cg nr" == "charge group number"
You've heard my thoughts on possible fundamental problems twice before.
It seems even more unlikely that your model physics was correctly
parameterized to suit TIP4P than a simpler water model. If it had been
correctly parameterized, you'd have a method in published literature to
be following. Apparently, you think you know best, so I'm going to stop
being helpful. :-)
Mark
> On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 26/03/2010 7:03 AM, Gareth Tribello wrote:
>
> Hello again
>
> I have tried to do as you suggest and use tables but I have a new
> problem. First let me describe my process and then you can let
> me know
> if there is anything wrong in the stages:
>
> OK so first you include the following directives into the mdp file:
>
> coulombtype = pme (or whatever sort of coulomb interaction you
> are using)
> vdw-type = user
>
> energygrps = Ca CCA OCA OW HW
> energygrp_table = Ca OCA Ca CCA OCA OCA OCA OW OCA HW
>
> Gromacs is then (at some stage) going to look for a series of
> files called
>
> table.xvg - which is the default 6-12 Lennard Jones that will
> be used
> for most of the atoms
> table_Ca_OCA.xvg - which are the Buckingham interactions
> between your
> various atom types.
> table_Ca_CCA.xvg
> table_OCA_OCA.xvg
> table_OCA_OW.xvg
> table_OCA_HW.xvg
>
> These files have the format (and contents) described in section
> 6.7 of
> the manual. Finally, you define the various energy groups Ca,
> OCA and
> so on in your index.ndx file.
>
> The problem is that grompp gives me the following error:
>
> "atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in
> different
> energy groups"
>
> (incidentally these atoms 1 and 2 are OW and HW)
>
> Does this mean that I cannot use different tabulated potentials for
> different atoms in a molecules? By which I mean that I can't use
> different tabulated potentials for the OW Ca and HW Ca
> interactions for
> example?
>
>
> Charge groups are the fundamental unit GROMACS uses in constructing
> a simulation. Energy groups are the next "higher" layer in the data
> structures, and these must be sets of whole charge groups. With some
> electrostatics models, looping over charge groups whose charge is
> preferably an integer is essential for modelling correct behaviour.
> GROMACS does a complex sorting of all the interactions between
> charge groups into lists that allow it to iterate over charge groups
> and energy groups. A user table then gets applied to a whole intra-
> or inter- energy-group loop. Thus your attempt violates this
> precondition.
>
> However, PME does not require the use of charge groups for accurate
> results, since all inter-atomic electrostatic interactions get
> treated, regardless of distance. So you could decompose your water
> molecules into two charge groups, O and Hs. (Caveat, a near-brokenly
> bad PME approximation might get a little worse with arbitrary charge
> groups)
>
>
> Final question, as its not clear to me from the manual, if you use a
> tabulated potential for Lennard Jones and you use mix type 2 (so
> are you
> are providing epsilon and sigma in the input rather than A and
> B) does
> gromacs still know that it has to manipulate the input parameters in
> order to get the coefficients of the (tabulated) g(r) and h(r)
> dispersion and repulsion functions (I mean the g(r) and h(r)
> defined in
> section 6.7 of the manual here)? At the same time does it also
> know not
> to do anything to the parameters you input for the (tabulated)
> buckingham potentials (as for a buckingham you are providing A
> and C)?
>
>
> I expect the point of the tables is that GROMACS just uses them per
> equation 6.23. Thus I'd expect C6 and C12 in that equation to be
> constructed according to whatever combination rule is in force. If
> you've specified them explicitly in the topology (see chapter 5),
> then they will not be constructed.
>
> You should be very careful to test your assumptions and deductions
> about how all this machinery is working. Do take the time to set up
> a tabulated version of a quick non-tabulated calculation to at least
> make sure you've done the simple things right! To test the function
> of eq 6.23, do a non-table constructed-parameter calculation, a
> non-table topology-specified-parameter calculation, a table
> constructed-parameter calculation, etc. to be sure you understand
> what is going on - and that the code works right! Please consider
> contributing any insights to a wiki page on the GROMACS webpage.
>
> Before you go to all this work please consider my advice of last
> email. Unless you have an existing reason to expect some ad-hoc
> combination of different interaction functions to work well
> together, you may find that your best possible result is a
> correctly-functioning random number generator.
>
> Mark
>
> On Wed, Mar 24, 2010 at 2:25 AM, Mark Abraham
> <mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>> wrote:
>
>
>
> ----- Original Message -----
> From: Matthew Watkins <matthew.watkins at ucl.ac.uk
> <mailto:matthew.watkins at ucl.ac.uk>
> <mailto:matthew.watkins at ucl.ac.uk
> <mailto:matthew.watkins at ucl.ac.uk>>>
> Date: Wednesday, March 24, 2010 2:59
> Subject: Re: [gmx-users] Using lennard jones and buckingham
> terms
> simultaneously
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
>
> > Hi Gareth,
> >
> > as Vitaly suggested tabulated potentials seem to be the only way
> > to go, it took me a while to get up to speed on the Gromacs way
> > of doing this, so get in touch if you wish.
> >
> > The tables for buck potentials need to include the standard 1/r6
> > term whilst what would be the 1/r12 term needs to contain exp(-
> > Bx.rho), the C6 and C12 coefficients can then be put in a
> > standard nonbonded section. You'll need a separated table
> > for each pair of interactions that interact with buckingham
> > potential. Each pair must be an energy group as well.
> >
> > If there is a simpler method I'd love to hear it.
>
> There's probably not a simpler method because it's not a
> widely-used
> procedure. It shouldn't be used at all unless you have
> established
> that the combination of functional forms is effective...
>
> Mark
> --
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