[gmx-users] Assigning mass to a virtual site

[Justin Lemkul]

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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