[gmx-users] Assigning mass to a virtual site
David van der Spoel
spoel at xray.bmc.uu.se
Wed Oct 29 14:00:27 CET 2014
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.
--
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
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