[gmx-users] Assigning mass to a virtual site

[David van der Spoel]

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.

>
> 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).
>
> Thanks for your assistance!
>
> Regards,
> Kester
>
>
>
>
> --------- 원본 메일 ---------
>
>     *보낸사람* : Justin Lemkul <jalemkul at vt.edu>
>     *받는사람* : <gmx-users at 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 at 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.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se