[gmx-users] Forcefield parameters

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 28 08:57:08 CEST 2010


On 28/10/2010 3:03 AM, 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"?
No, [pairtypes] are not relevant.
> 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...

I was thinking of a flawed procedure. Ignore this part.

Mark

> 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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