Hello gain Justin, Now I figured out that the problem was in gromacs version 4.0. So peptide in water works no problem.
I have used trjconv -pbc mol -ur compact and it solved the artifact problem. Thanks a lot! Now I have started simulation on 96 CPU's for 1000ns total run time. But after 1 day simulation the system crashed or exploded with the following error: [First time it failed because of some problems with the server, and then I have resumed the run using tpbconv -s DMPCRun1000ns.tpr -f 1000nsDMPCA141Run_part1.trr -extend 100000 -o DMPCRun100nspart2.tpr] vol 0.78 imb F 2% pme/F 2.15 step 10578400, will finish Sat Aug 29 07:23:01 2009 vol 0.77 imb F 3% pme/F 2.15 step 10578500, will finish Sat Aug 29 07:28:32 2009 Step 10578599, time 21157.2 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.299801, max 6.073617 (between atoms 9449 and 9450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9451 9468 93.6 0.1530 0.1293 0.1530 Fatal error: 15 particles communicated to PME node 6 are more than a cell length out of the domain decomposition cell of their charge group I am attaching my mdp files used to to EM and MDrun here: EM: http://kbessonov.googlepages.com/em_lipid.mdp MD: http://kbessonov.googlepages.com/mdonly_1000ns.mdp I was wondering why my system fails. and what can I do to avoid it? I was thinking maybe to run several times EM on the system, maybe it will help? What bugs me is that it fails really late in simulation. I have not seen trajectory file yet.
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