<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Dear David, </p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><b>보낸사람</b> : David van der Spoel <spoel@xray.bmc.uu.se><br><b>받는사람</b> : <gmx-users@gromacs.org><br><b>받은날짜</b> : 2014년 10월 29일(수) 23:27:19<br><b>제목</b> : Re: [gmx-users] Assigning mass to a virtual site<br><!-- original content --><div style="margin-top:5px;"><pre>On 2014-10-29 14:50, Kester Wong wrote:
> Dear David and Justin,
>
> The SWM4-NDP force field was downloaded from virtualchemistry correct,
> but the non-polarisable version of the OH(with virtual sites) is not
> available, to the best of my knowledge.
But we did not publish that either.
</pre></div></div></blockquote>The non-polarisable hydroxide parameters were described, albeit not in full details in the paper, the supporting material does contain the hydroxide non-bonded parameters as follows:</p><p style="margin-bottom: 0px; margin-top: 0px;"><font face="monospace"><span style="line-height: 20px;">http://www.biophysj.org/biophysj/supplemental/S0006-3495(14)00566-9</span></font></p><p style="margin-bottom: 0px; margin-top: 0px;"><font face="monospace"><span style="line-height: 20px;"></span><br><span style="font-family: Gulim; font-size: 12px; line-height: 18px; white-space: pre;">Is there a particular reason why the hydroxide topology file is not published (as was made available in the hydronium HYDYN paper)? </span></font></p><p style="margin-bottom: 0px; margin-top: 0px;"><br></p><p style="margin-bottom: 0px; margin-top: 0px;"><blockquote style="font-family: Gulim; font-size: 12px; line-height: 1.5; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
>
> The section that describes the 1 a.m.u mass at the virtual site is
> available in the supporting material of the paper by Wolf et al. I will
> ask Wolf et al. and try to obtain the topology directly from the authour(s).
http://virtualchemistry.org/pol.php
(I am the author).</pre></div></div></blockquote><font face="monospace">Yes I am aware of that, but I am referring to this paper by Wolf, Grubmuller, and Groenhof: Anomalous Surface Diffusion of Protons on Lipid Membranes,<br><span style="font-size: 12px; line-height: 18px; white-space: pre;">that employed the </span></font><span style="font-family: monospace;">non-polarisable hydroxide model. Here, the hydroxide was modeled very similarly to the polarisable version.</span></p><p style="margin-bottom: 0px; margin-top: 0px;"><br></p><p style="margin-bottom: 0px; margin-top: 0px;">Anyway, I hope that someone could share some information concerning the assignment of the atomic number of a virtual site. Thanks!</p><p style="margin-bottom: 0px; margin-top: 0px;"><br></p><p style="margin-bottom: 0px; margin-top: 0px;"><br></p><p style="margin-bottom: 0px; margin-top: 0px;"><span style="font-family: monospace;"></span><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;">Regards,</span></font></p><p style="margin-bottom: 0px; margin-top: 0px;"><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;">Kester<br></span></font><blockquote style="font-family: Gulim; font-size: 12px; line-height: 1.5; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
>
> Thanks for your assistance!
>
> Regards,
> Kester
>
>
>
>
> --------- 원본 메일 ---------
>
> *보낸사람* : Justin Lemkul <jalemkul@vt.edu>
> *받는사람* : <gmx-users@gromacs.org>
> *받은날짜* : 2014년 10월 29일(수) 22:14:12
> *제목* : Re: [gmx-users] Assigning mass to a virtual site
>
> On 10/29/14 9:00 AM, David van der Spoel wrote:
> > On 2014-10-29 13:19, Justin Lemkul wrote:
> >>
> >>
> >> On 10/29/14 6:32 AM, Kester Wong wrote:
> >>> Dear all,
> >>>
> >>>
> >>> I am creating a topology file for hydroxide, closely following the
> >>> parameters
> >>> from the paper by Wolf et al:
> >>>
> >>> http://dx.doi.org/10.1016/j.bpj.2014.04.062
> >>>
> >>>
> >>> This is somewhat similar to the polarisable hydroxide topology that
> >>> was included
> >>> in the recent SWM4-NDP force field.
> >>>
> >>>
> >>> In this non-polarisable topology, I would like to know what atomic
> >>> number should
> >>> one label for the OH-OV2 type atom, as it was defined as a virtual
> >>> site (but
> >>> with 1 a.m.u assigned) in the paper's supporting material. I have
> >>> labeled the
> >>> atomic number with "X" as below:
> >>>
> >>>
> >>> [ atomtypes ]
> >>>
> >>> ;name at.num mass charge ptype sigma epsilon
> >>>
> >>> OH-O 8 11.9980 -1.32 A 0.00 0.00
> >>>
> >>> OH-H 1 1.00800 0.00 A 0.14 0.2150576
> >>>
> >>> OH-OV1 0 0.00000 0.00 D 0.2916 0.2150576
> >>>
> >>> OH-OV2 X 1.00000 0.00 A 0.25 0.2150576
> >>>
> >>> OH-qH 0 0.00000 0.32 D 0.00 0.00
> >>>
> >>>
> >>> Can an atom (ptype=A) have zero at.num?
> >>>
> >>
> >> I would suggest you simply ask the authors to provide you with their
> >> topology. There are several details that are unclear to me, and I do not
> >> see anything that says the V1 or V2 sites carry any mass. Maybe I
> >> missed it due to a quick read-through, but this is in any case a very
> >> tricky setup. Don't reinvent the wheel; get the information straight
> >> from the people that did it.
> >>
> >> -Justin
> >>
> > The topology is correct as downloaded from virtualchemistry.org.
> >
>
> Good to know. I was afraid the OP was taking the hard way out and trying to do
> something from scratch that wasn't necessary :)
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
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</gmx-users@gromacs.org></jalemkul@vt.edu></pre></div><!-- original content --><br></div></blockquote></p></p>
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