[gmx-users] Assigning mass to a virtual site

[Justin Lemkul]

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

-- 
==================================================

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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