Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a model. I made several simulations changing the gen_seed in order to explore deeply the conformational space of the protein. I used a triclinic box (option editconf -bt triclinic -d 1 -c) filled with spc water and neutralized with ions; in my opinion, it's quite a standard system. I equilibrated the system with a minimization (emtol = 500 reached) and with NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the full MD for 30 ns, always at 310 K. I repeated this procedure (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers), starting from the same minimized structure. Obviously, in PR-NPT and full Md simulations, I did not recalculated the initial velocity (it's a continuation). Before starting with full MD I checked for energetic parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no apparent problems. I run the 30 ns simulations and now I'm checking for the results. Looking at the trajectories I see that in some (but not all) cases, the protein moves from the center of the box to one of the edges, starting from a time that is different in each simulation, when it happens. I run g_mindist, and in some cases (generally when the protein doesn't move so much) I see some "spikes" in the plot (that disappear if I apply trjconv -pbc nojump to the trajectory), but apart from these "spikes" the minimum periodic distance in the trajectory is at least 1.5 nm (I set van der Waals cut-off at 1.4 nm). In other cases, however (essentially when the protein starts moving towards the edges of the box), the minimum periodic distance starts decreasing (in some simulations after 10 ns, in some simulations after 20: there is not a common point after which you can see a sudden decrease of minimum periodic distance of the system) and reaches a value below 1.4 nm or even below 1 nm. Considering that the starting system is more or less the same in all cases, I don't identify the reason why the system "behaves" like this, and moreover what can I do to avoid this. My questions are: - do I have to enlarge the box? but I don't think that this would solve the "motion" of the protein towards one edge of the box - do I have to change the box? In his last message Tsjerk suggests to use a rhombic dodecahedron box, could it be useful in my case? - do you think it's a problem of stabilization of the system? Should I run a deeper minimization, or a longer NVT+NPT in my system? I'm quite puzzled especially because the system is the same in all cases, the only thing I changed in my simulations is the gen_seed. Could anybody give me some suggestions about it? Thank you very much Anna
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