[gmx-users] virtual sites in reference structure

[Ahmet yıldırım]

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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-- 
Ahmet Yıldırım