Dear Gromacs users, I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. Initially I pulled the ligand from extra to intracellular side of the protein. The pull code used are given below.
pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_rate1 = 0.005 pull_k1 = 1000 here group0 is one residue at the extracellular region and r_C1 is the side chain Carbon atom of the ligand. My question is , the total length of the channel is almost 40 Angstrom and as per my knowledge, when we did the pulling the pullx file will give the coordinate of the ligand through the channel. Even though ligand reaches the opposite end of the channel, in pullx file I am getting around 19 Angstrom in total. Again I calculate the g_dist of the ligand and the center of the channel, it shows around 40 Ang in total . Please find the links provided Am I misunderstanding anything about the pullx file. Could you please suggest me where thing get wrong? http://docs.google.com/fileview?id=0B1PyTWWGrqt6N2IyNjNhM2UtMzRiZC00MTJmLTg5ODItODJlMzQ5YTM3OGMy&hl=en http://docs.google.com/fileview?id=0B1PyTWWGrqt6ZWRlZGJkOTgtMGEwYi00MzE0LThiZTEtM2JjNmJkMWU5NDYy&hl=en Thank you, -- -Aswathy
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