I think I have not arrived to complete solution of my problem yet, but I think the cause of early LINCS warnings were version incompatibility. I am now trying to run simulation on the server that has only 4.0.5 Gromacs, will see if that helps and whether I will warnings in the middle of simulations.<br>
<br>I have tried PR simulation on peptide and it failed even earlier (after 10,000 steps), maybe this indicates version issues, as I would assume PR simulations are more stable as they does not allow peptide to enter DMPC layer ....<br>
<br>So after 20 ns of simulation on the server with Gromacs 4.0 I've started to get errors and LINCS warnings and simulation collapsed, I have resumed simualtion as per oldwiki instructions, but again it soon failed. After looking at the trajectory with VMD I see that the peptide "sinks" into DMPC and one phenyl ring flips out (Phe residue). Maybe due to local constrains and being surrounded by DMPC the errors start coming up. I am not sure. I will do the movie and post it on youtube as ato show you what is going on.<br>
<br>Why does the system fails after 10,578,600 steps? Is there way to ignore LINCS warnings and make simulation run anyways, if yes how?<br><br>I was not sure what to try next. Try to do several EM steps to get system to 500 kJ/mol, right now it is at 800 kJ/mol?<br>
<br>Or try to do longer equilibration steps by restraining protein using posre.itp file included in topology as per your tutorial?<br><br>Thanks for your time. <br>