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<div class="gmail_quote">On Wed, Oct 27, 2010 at 12:47 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Mark,<br> I am familiar with the section, however, I have a few doubts.<br> When you say ...<br>So modified protein-water VDW interactions can be introduced by defining all relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms.<br>
Do you mean that I can introduce [pairtypes] specifying interactions of all "relevant protein atoms" with "tip3p atoms"?<br> <br></blockquote><br></div>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:<br>
<br>"Some or all combinations for different atom types can be given in the<br>[ 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..."<br>
<br>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.
<div class="im"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> and I do not understand - It may be simpler to modify the [atomtypes] to generate the "modified" VDW from the combination rule<br>
Would this not alter all non-bonded interactions for the atomtypes defined? I think I haven't understood thsi properly...<br> <br></blockquote><br></div>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.<br>
</blockquote>
<div> </div>
<div>Thanks Justin. That clarifies everything.</div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> Pooja
<div class="im"><br><br> On Tue, Oct 26, 2010 at 8:21 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>> wrote:<br>
<br> I think manual 5.3.3 covers the relevant points. Let me know what is<br> not clear.<br><br> Mark<br><br><br> ----- Original Message -----<br></div>
<div class="im"> From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a> <mailto:<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>>><br> Date: Wednesday, October 27, 2010 9:41<br>
Subject: Re: [gmx-users] Forcefield parameters<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
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<div class="h5"> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br><br> ><br> ><br> > On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham<br> <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>> wrote:<br>
<br> ><br> ><br> > ----- Original Message -----<br> > From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br> > Date: Wednesday, October 27, 2010 8:52<br>
> Subject: Re: [gmx-users] Forcefield parameters<br> > To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br> ><br>
> > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br><br> > ><br> > ><br> > > Sai Pooja wrote:<br>
<br> > ><br> > ><br> > > On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
> ><br> > ><br> > ><br> > > Sai Pooja wrote:<br> > ><br> > > Hi,<br> > > I want to change the non-bonded parameters<br>
to modify the<br> > > interaction between water molecules and<br> protein molecules.<br> > > I am using CHARMM forcefield with Tip3p water.<br>
> > The ffnonbonded.itp file of the forcefield<br> has non-bonded<br> > > parameters for tip3p water. Can I achieve<br> the above by changing<br>
> > these parameters?<br> > > > ><br> > > That depends on your definition of "modify," but<br> yes, in a way, you<br>
> > can make changes here.<br> > > 1) Modify - Multiply sigma and epsilon by a constant<br> > ><br> > > If yes, will this also change the non-bonded<br>
parameters for<br> > > water - water interaction?<br> > ><br> > > 2) Is there a way to add a new ifdef perhaps such<br> that a modified sigma and epsilon can be used for<br>
water-protein interactions and the unmodified parameters<br> can be used for water-water interactions?<br> > > <br> > ><br> > > Nonbonded interactions are calculated during the<br>
simulation by applying the combination rules defined by the<br> force field. There is no simple way to do this with an<br> ifdef, since that is just in the topology. You can't<br> conditionally apply nonbonded parameters. That just sounds<br>
like a recipe for breaking a force field.<br><br> ><br> > Not quite right. Parameters for VDW are calculated from the<br> combination rules from the atom-specific values given in<br> [atomtypes] only as a last resort. [nonbond_params] are used in<br>
preference to such.<br> ><br> > So modified protein-water VDW interactions can be introduced<br> by defining all relevant "protein atom"-"TIP3P oxygen"<br> [nonbond_params] terms. It may be simpler to modify the<br>
[atomtypes] to generate the "modified" VDW from the combination<br> rule, and introduce the "normal" TIP3P oxygen-oxygen interaction<br> via [nonbond_params].<br><br> > > Mark, could you please elaborate the method?<br>
<br> ><br> > Mark<br> > --<br> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<div class="im">========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- <br></div>
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