[gmx-users] Forcefield parameters

[Justin A. Lemkul]

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.

-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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