[gmx-users] Peptide - DMPC membrane simulations -> Unstable system

Kirill Bessonov kbessonov at gmail.com
Mon Jul 20 22:04:37 CEST 2009

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.

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 ....

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.

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?

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?

Or try to do longer equilibration steps by restraining protein using
posre.itp file included in topology as per your tutorial?

Thanks for your time.
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