[gmx-users] About periodic image of system.......
ramadavidgroup at gmail.com
Sat Nov 10 16:02:27 CET 2012
Thank you for your reply and explanation,
My ligand is protein( 4 amino acid peptide).
The group in index file PROTEIN contain both ligand
The box size is 11.4942 10.7884 10.7884 at the time 16162 (ps).
The box size I given in editconf is 11.40000 10.70000 10.70000
So please would you told me the reason for my g_mindist value less than vdw
cut off 1.4 ?????
With best wishes and regards,
On Sat, Nov 10, 2012 at 7:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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