[gmx-users] Forcefield parameters
Sai Pooja
saipooja at gmail.com
Wed Oct 27 18:57:45 CEST 2010
On Wed, Oct 27, 2010 at 12:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Sai Pooja wrote:
>
>> Hi Mark,
>> I am familiar with the section, however, I have a few doubts.
>> When you say ...
>> So modified protein-water VDW interactions can be introduced by defining
>> all relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms.
>> Do you mean that I can introduce [pairtypes] specifying interactions of
>> all "relevant protein atoms" with "tip3p atoms"?
>>
>>
>
> The [pairtypes] directive is for intramolecular interactions (1-4
> interactions), not intermolecular interactions. The proper directive to
> add/modify is [nonbond_params], as Mark said. Section 5.3.3 clearly
> describes the mechanism by which nonbonded interactions are calculated:
>
> "Some or all combinations for different atom types can be given in the
> [ nonbond_params ] section. Any combination that is not given will be
> computed from the parameters for the corresponding atom types, according to
> the combination rule..."
>
> So, if there are no entries for the interaction in [nonbond_params], that
> interaction is calculated. If there are parameters defined in
> [nonbond_params], then it is not calculated. This mechanism allows you to
> define whatever modified terms you want in [nonbond_params]. Anything you
> don't want modified (i.e. water-water interactions) will be calculated
> according to the combination rules.
>
>
> and I do not understand - It may be simpler to modify the [atomtypes] to
>> generate the "modified" VDW from the combination rule
>> Would this not alter all non-bonded interactions for the atomtypes
>> defined? I think I haven't understood thsi properly...
>>
>>
>
> Any change to the [atomtypes] directive will be a global change, modifying
> all nonbonded interactions, which, from your earlier posts, sounds like
> something you don't want to be doing.
>
Thanks Justin. That clarifies everything.
>
> -Justin
>
> Pooja
>>
>>
>> On Tue, Oct 26, 2010 at 8:21 PM, Mark Abraham <mark.abraham at anu.edu.au<mailto:
>> mark.abraham at anu.edu.au>> wrote:
>>
>> I think manual 5.3.3 covers the relevant points. Let me know what is
>> not clear.
>>
>> Mark
>>
>>
>> ----- Original Message -----
>> From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at gmail.com>>
>> Date: Wednesday, October 27, 2010 9:41
>> Subject: Re: [gmx-users] Forcefield parameters
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>
>>
>> >
>> >
>> > On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham
>> <mark.abraham at anu.edu.au> wrote:
>>
>> >
>> >
>> > ----- Original Message -----
>> > From: Sai Pooja <saipooja at gmail.com>
>> > Date: Wednesday, October 27, 2010 8:52
>> > Subject: Re: [gmx-users] Forcefield parameters
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >
>> > > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul
>> <jalemkul at vt.edu> wrote:
>>
>> > >
>> > >
>> > > Sai Pooja wrote:
>>
>> > >
>> > >
>> > > On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>> > >
>> > >
>> > >
>> > > Sai Pooja wrote:
>> > >
>> > > Hi,
>> > > I want to change the non-bonded parameters
>> to modify the
>> > > interaction between water molecules and
>> protein molecules.
>> > > I am using CHARMM forcefield with Tip3p water.
>> > > The ffnonbonded.itp file of the forcefield
>> has non-bonded
>> > > parameters for tip3p water. Can I achieve
>> the above by changing
>> > > these parameters?
>> > > > >
>> > > That depends on your definition of "modify," but
>> yes, in a way, you
>> > > can make changes here.
>> > > 1) Modify - Multiply sigma and epsilon by a constant
>> > >
>> > > If yes, will this also change the non-bonded
>> parameters for
>> > > water - water interaction?
>> > >
>> > > 2) Is there a way to add a new ifdef perhaps such
>> that a modified sigma and epsilon can be used for
>> water-protein interactions and the unmodified parameters
>> can be used for water-water interactions?
>> > >
>> > >
>> > > Nonbonded interactions are calculated during the
>> simulation by applying the combination rules defined by the
>> force field. There is no simple way to do this with an
>> ifdef, since that is just in the topology. You can't
>> conditionally apply nonbonded parameters. That just sounds
>> like a recipe for breaking a force field.
>>
>> >
>> > Not quite right. Parameters for VDW are calculated from the
>> combination rules from the atom-specific values given in
>> [atomtypes] only as a last resort. [nonbond_params] are used in
>> preference to such.
>> >
>> > So modified protein-water VDW interactions can be introduced
>> by defining all relevant "protein atom"-"TIP3P oxygen"
>> [nonbond_params] terms. It may be simpler to modify the
>> [atomtypes] to generate the "modified" VDW from the combination
>> rule, and introduce the "normal" TIP3P oxygen-oxygen interaction
>> via [nonbond_params].
>>
>> > > Mark, could you please elaborate the method?
>>
>> >
>> > Mark
>> > --
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>> >
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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