[gmx-users] meaning of minus potential and buried surface area
ahmedo047 at gmail.com
Thu Sep 22 16:59:39 CEST 2011
If possible, can you some explain "net attraction"?
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.
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users