[gmx-users] number of contact

[Justin A. Lemkul]

On 7/2/12 8:18 AM, Turgay Cakmak wrote:
> Dear all,
>
> Does the "number of contact calculated by g_mindist" mean that
> interaction between two groups? If so, could you kindly check the
> reliability of the case I have written below.
>

If the atoms are in contact within a given cutoff distance, then you can pretty 
safely assume they are interacting (provided the cutoff is not exorbitantly 
long, but 0.4 nm seems reasonable).

-Justin

> I have 10 peptides (5 of them are X-peptide and 5 of them are
> Y-peptide) in a box filled with water. After MD simulation (production
> run), I saw all the peptides come together. Now, in order to
> understand whether
> hydrophobic forces are important for this aggregation or not, I
> calculated number of contacts between 2 index groups (First group
> consist of hydrophobic residues (FFAA) belong to X-peptide and
> second group again consist of hydrophobic residues (FFAA) belong to
> Y-peptide) using the following command;
>
> g_mindist -f .xtc -s .tpr -n .ndx -on -d 0.4
>
> Then, when I looked the number of contact versus time graph, there is
> an increase in the number of contact over time. (I think this makes
> sense in the aggregation case.)
> Thanks in advance,
>
> Turgay
>

-- 
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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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