[gmx-users] About periodic image of system.......

[Justin Lemkul]

On 11/10/12 8:44 AM, rama david wrote:
> Hi justin ,
> Thank you for reply.
> Mdp parameters are as follow ,
>
> ; Neighborsearching
> ns_type        = grid        ; search neighboring grid cells
> nstlist        = 5        ; 10 fs
> rlist        = 0.9        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9        ; short-range electrostatic cutoff (in nm)
> vdw-type        = Cut-off
> rvdw        = 1.4        ; short-range van der Waals cutoff (in nm)
>
> I choose the protein for g_mindist option..
>
> Please could you explain me what am getting and why it is not violation of
> pbc????
>

Before you said you had a protein and ligand.  Is the ligand itself actually a 
protein?

PBC artifacts arise when you violate the minimum image convention, that is, the 
same interaction is calculated multiple times, thus leading to erroneous 
contributions to the forces and flawed dynamics.  If you avoid double-counting 
of interactions by setting an appropriately sized box, these don't occur.

The only way I would see any spurious interactions occurring in your case is if 
the box massively shrank (which probably would have caused the system to crash 
anyway) or if any protein molecules unfolded.  Stable, well-folded proteins 
placed in suitably sized boxes generally do not experience PBC artifacts, and 
the evidence you have presented thus far is not indicative of any problem.

-Justin

-- 
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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

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