[gmx-users] Using lennard jones and buckingham terms simultaneously
Gareth Tribello
gareth.tribello at gmail.com
Tue Mar 30 16:40:00 CEST 2010
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 obviously missing something fundamental - I'm not even sure that cg nr
stands for the charge group. Any help would be greatly appreciated.
Gareth
On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham <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>> wrote:
>>
>>
>>
>> ----- Original Message -----
>> From: Matthew Watkins <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>>
>>
>> > 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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