[gmx-users] meaning of minus potential and buried surface area

[ahmet yıldırım]

Dear Justin,

If possible, can you some explain "net attraction"?

Best regards

2011/9/22 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> 1.) During the simulation the mean potential energy is minus (-) value.
>> What does this mean? Why minus?
>>
>
> Net attraction.
>
>
>  2.) let's say, Interface/Buried Surace Area (ISA) between protein and
>> ligand was calculated and hydrophobic ISA obtained greater than hydrophilic
>> ISA. What does this mean?
>>
>>
> That, as you might expect, hydrophobic groups are shielded from the solvent
> to a greater extent than polar groups.
>
> -Justin
>
>
>  No one is my special advisor but If you help me, I will be happy.
>>
>> Thanks in advance
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 YILDIRIM
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