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.
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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
