[gmx-users] Peptide - DMPC membrane simulations -> Unstable system
Justin A. Lemkul
jalemkul at vt.edu
Tue Jul 21 00:01:33 CEST 2009
Kirill Bessonov wrote:
> 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 ....
Right; rule out the version as a problem first.
> 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.
So does this "sinking" behavior always correlate with a LINCS crash? Or is the
crashing sporadic? I wouldn't base any conclusions based on 4.0 simulations -
get results from 4.0.5 before diagnosing.
> 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?
LINCS warnings cannot be ignored. They indicate instability in the system,
either because of a bug (one that I identified in version < 4.0.2), or because
your method of running the simulation is incorrect (force field, .mdp
parameters, system preparation, etc). Note that I commented on your treatment
of temperature and pressure coupling, as well as COM motion removal previously
as being potentially problematic.
> 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?
It may or may not be feasible to achieve an Fmax this low. I think 800 is fine;
many systems that run stably do not even get this low, in my own experience.
> Or try to do longer equilibration steps by restraining protein using
> posre.itp file included in topology as per your tutorial?
I really think proper equilibration is necessary (with restraints on the
protein). Never have I seen anyone report in the literature, "following energy
minimization, unrestrained simulations were initiated and data collection
begun." I would seriously question that methodology (see my comments in
> Thanks for your time.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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