<div>Hi Mark,</div>
<div> </div>
<div>I am familiar with the section, however, I have a few doubts.</div>
<div> </div>
<div>When you say ...</div>
<div>So modified protein-water VDW interactions can be introduced by defining all relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms.</div>
<div>Do you mean that I can introduce [pairtypes] specifying interactions of all "relevant protein atoms" with "tip3p atoms"?</div>
<div> </div>
<div> </div>
<div>and I do not understand - It may be simpler to modify the [atomtypes] to generate the "modified" VDW from the combination rule</div>
<div>Would this not alter all non-bonded interactions for the atomtypes defined? I think I haven't understood thsi properly...</div>
<div> </div>
<div> </div>
<div>Pooja</div>
<div><br> </div>
<div class="gmail_quote">On Tue, Oct 26, 2010 at 8:21 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">I think manual 5.3.3 covers the relevant points. Let me know what is not clear.<br><font color="#888888"><br>
Mark</font>
<div><br><br>----- Original Message -----<br>From: Sai Pooja <<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>><br></div>
<div>
<div></div>
<div>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>
<br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br>
<div class="gmail_quote"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham <span dir="ltr"><<a>mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>----- Original Message -----<br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>From: Sai Pooja <<a>saipooja@gmail.com</a>><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>Date: Wednesday, October 27, 2010 8:52<br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>Subject: Re: [gmx-users] Forcefield parameters<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>To: Discussion list for GROMACS users <<a>gmx-users@gromacs.org</a>><br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br>
<div class="gmail_quote"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font>On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul <span dir="ltr"><<a>jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font>Sai Pooja wrote:
<div><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font>On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul <<a>jalemkul@vt.edu</a> <mailto:<a>jalemkul@vt.edu</a>>> wrote:<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> Sai Pooja wrote:<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> Hi,<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> I want to change the non-bonded parameters to modify the<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> interaction between water molecules and protein molecules.<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> I am using CHARMM forcefield with Tip3p water.<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> The ffnonbonded.itp file of the forcefield has non-bonded<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> parameters for tip3p water. Can I achieve the above by changing<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> these parameters?<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> <br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> That depends on your definition of "modify," but yes, in a way, you<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> can make changes here. <br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> 1) Modify - Multiply sigma and epsilon by a constant<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> If yes, will this also change the non-bonded parameters for<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> water - water interaction?<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font>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?<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font> <br>
</blockquote><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font><br>
</div><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>> </font>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.<br>
</blockquote></div><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br></div><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>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.<br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>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].<br>
</blockquote>
<div><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font> </div>
<div><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>Mark, could you please elaborate the method?</div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><font color="#888888"><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font><br>
<font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>Mark </font><br><font style="FONT-WEIGHT: normal; FONT-SIZE: 14px; FONT-STYLE: normal; BACKGROUND-COLOR: rgb(245,248,240)">> </font>--<br>
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