[gmx-users] virtual sites in reference structure

[Tsjerk Wassenaar]

Hi Ahmet,

What is an incorrect RMSD? What is a correct RMSD? If you want to
calculate a backbone RMSD and you include side chain atoms, that's
wrong. Likewise, if you want to calculate a heavy atom, or
protein-all-atom RMSD and include virtual sites, that's wrong. If you
want to calculate an all-particle RMSD and you include virtual sites,
that's correct. If you do a mass-weighted RMSD, the contributions of
(those) virtual sites are always zero, because they don't have mass.
For the SASA, it's a bit of a different story. The area of a virtual
site should be zero, but I'm not sure if that's handled correctly. If
the virtual site is identified as unknown atom, then it is assigned a
default radius, which will give wrong results. But it's easy to
circumvent by choosing proper index groups.

Hope it helps,

Tsjerk

On Thu, Feb 21, 2013 at 9:33 AM, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:
> Dear Tsjerk,
>
> Do the virtual sites cause incorrect calculations of SASA, RMSD or something
> else?
>
> Regards
> 2013/2/21 Tsjerk Wassenaar <tsjerkw at gmail.com>
>
>> Hi Ahmet,
>>
>> You can always use suitable index groups for analysis.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım <ahmedo047 at gmail.com>
>> wrote:
>> > I thought the virtual sites can affect analysis.For example, dont they
>> cause
>> > incorrect calculations of SASA, RMSD or something else?
>> >
>> > Thanks in advance
>> >
>> > 2013/2/20 Justin Lemkul <jalemkul at vt.edu>
>> >
>> >>
>> >>
>> >> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
>> >>
>> >>> Dear users,
>> >>>
>> >>> I have the virtual sites in reference structure and all trajectory.
>> When
>> >>> analyzing simulation, do I have to get rid of those(virtual sites)? If
>> >>> yes/no, why?
>> >>>
>> >>>
>> >> Why do you think you need to remove them?
>> >>
>> >> -Justin
>> >>
>> >> --
>> >> ==============================**==========
>> >>
>> >> Justin A. Lemkul, Ph.D.
>> >> Research Scientist
>> >> Department of Biochemistry
>> >> Virginia Tech
>> >> Blacksburg, VA
>> >> jalemkul[at]vt.edu | (540) 231-9080
>> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>
>> >> ==============================**==========
>> >> --
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>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Biocomputing Group
>> Department of Biological Sciences
>> 2500 University Drive NW
>> Calgary, AB T2N 1N4
>> Canada
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>
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> Ahmet Yıldırım
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada