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

[rama david]

Dear justin,

Thank you for your reply and explanation,

My ligand is protein( 4 amino acid peptide).
The group in index file PROTEIN  contain both ligand
and protein.

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,
Rama david



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
>> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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