I was trying to do the steered MD on a membrane-protein system. The 60 ns pre-equilibration seemed nothing wrong. The average temperature and pressure reached the expected value. But when I did the pulling, I kept getting the following error after many steps and the program corrupted. I have tried to change coupling methods or minimize dt to 0.00001 ps (thought maybe there were inappropriate atomic contacts during the pulling), but none of this helped. Anyone knows why? I would really appreciate your help.
Step 59700: The total potential energy is -nan, which is not finite. The LJ
and electrostatic contributions to the energy are 242.928 and -2996.67,
respectively. A non-finite potential energy can be caused by overlapping
interactions in bonded interactions or very large or Nan coordinate values.
Usually this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology.
You can check your pulling setting (e.i pull-coord1-rate [nm/ps]) in mdp file. Maybe you are pulling too fast or the wrong group and two atoms come too close or bonded atoms are overlapping .
Thanks for your suggestion. Below is my pulling setting. I suppose the pulling rate is sufficiently low. The group fixCA is freezed while the group testCA is pulled. These two groups are two Ca2+ ions. I guess the setting is ok?
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = testCA
pull_group2_name = fixCA
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.0001 ; 0.0001 nm per ps = 0.1 nm per ns
pull_coord1_k = 2000 ; kJ mol^-1 nm^-2
pull-nstxout = 50
pull-nstfout = 50
The message that you got implied that you have a problem in the bonded interactions. As far as I understood you are pulling two Calcium ion apart from each other. I assume that two Ca2+ ions are not covalently bonded to the protein or other. Thus you can check if the pulling group are correctly define in index file (CA atom name is used also for C_alpha, that may cause some misunderstanding in the generation of index file); you can get if you get information in log file on which bonded interactions have problems; you can check if you Ca2+ atoms are locked in the protein along z, you can try to use different pull option (e.i pull_coord1_geometry).
I hope this help