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
--
========================================
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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