[gmx-users] virtual sites in reference structure

[Tsjerk Wassenaar]

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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>
>
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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