Dear Gromacs users, I am doing simulations in HII phase in absence of any sugar or alkane to fill the gaps (in other words, HII in water) In few of my systems (which I made), there are lipids which their tails have bad contacts. Based on visualization, the CH2-CH2 bond from one tail in lipid 1 cross the CH2-CH2 bond in the tail from an adjacent lipid. They kinda stuck there.
Interestingly, these systems are running properly during EM step, as well as MD with a time step of 1 fs but fail with 2 fs, even after 45 ns of simulation with 1 fs. The lipid-lipid contacts cause LINCS errors for angles on those bonds and involved hydrogens, and eventually, the system will blow up. This is what I understand after many tests to figure out the problem for this failure (segmentation fault (core dumped)). The topology of the molecule is correct and there is not water molecule which causes the problem. I also did simulations on one lipid both in the vacuum and in water. Everything is fine. The system setup is the only thing which I am suspicious about. Is there any trick to: 1) recognize these bad contacts? (I deleted few lipids but still, there are other lipids which cause the problem) 2) remove these bad contacts? (applying stronger bond and angle force constant, changing the LINCS parameters, or something like these?) I highly appreciate your help in advance, Cheers Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.