Hi all,
My system has got BLOWING UP . I followed the protocol in http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below: Step 1: If the crash is happening relatively early (within a few steps), set nstxout (or nstxtcout) to 1, capturing all possible frames. Watch the resulting trajectory to see which atoms/residues/molecules become unstable first. I got this warning: Warning: 1-4 interaction between 5 and 18 at distance 2.003 which is larger than the 1-4 table size 2.000 nm Step 2: Simplify the problem: If you have a new box of solvent, try minimizing and simulating a single molecule to see if the instability is due to some inherent problem with the molecule's topology or if instead there are clashes in your starting configuration. I got this: Now there are 24 residues with 360 atoms Making bonds... Warning: Long Bond (1-18 = 0.357049 nm) Step 3: Monitor various components of the system's energy using g_energy. If an intramolecular term is spiking, that may indicate improper bonded parameters, for example. The improper-dihedral plot is strange. It "goes up in first picoseconds" and then goes down slightly. I think there is something wrong in dihedrals which I defined in .rtp file in the new residue. atom 18 is the H atom of formyl ( Formyl is as the N-terminus and is connected to a Valine residue) Now , what do I need to do? Going to the next step of diagnosing? or no? How can I fix the problem? Would you mind helping me please and give me suggestions? Thanks in advance. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
