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
previous messages).
-Justin
Thanks for your time.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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