[gmx-users] About periodic image of system.......
jalemkul at vt.edu
Sat Nov 10 14:56:00 CET 2012
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
Before you said you had a protein and ligand. Is the ligand itself actually a
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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