Bing Bing wrote:
My protein complex was minimized initially before putting into the
lipid. POPC is also a preequilibrated structure from Tielemen website. I
don't quite understand on what you meant by "the protein is not happy
with the restraint". The system went well through out the nvt, npt with
I think what Mark was getting as was if you're restraining some unusual or
inappropriate geometry, you can get nasty results when you turn off restraints.
I don't know that this is the case in your situation.
restraint on protein.... Once it move to md production run ( which is
without restraint on protein), error occurred (range checking error).
The reason i'm using the version3.3.2 is because the forcefield i'm
using at the moment only support version3.3.2. Is my problem cause by
I don't understand this statement. The force field you mentioned is most
certainly supported in the newest version of Gromacs, in fact my tutorial was
written for the version 4.0.x series. Please also see the advanced
troubleshooting page I provide; you may find some ideas there.
Certainly, watch the trajectory and see where things are going wrong to deduce
the nature of the issue.
-Justin
bug of the older version? is there any bugfix fot this? please
help.
regards,
Bing
On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
Bing Bing wrote:
Dear All,
I'm running the protein complex with POPC system. NVT (100ps)
and NPT (200ps) were done with restraint on the protein follow
by 1000 ps of NPT without restraint on protein. The trajectory
was checked in term of pressure, potential, area per lipid
....were checked and everything seems ok (potential almost
plateu, area per lipid close to experimental value). I proceeded
with md (similar to Justin's tutorial) for 1 ns. The simulation
stop around 800ps with the range checking error.
OK so look at the collective variables, and/or trajectory to find
evidence of the problem. The most likely explanation is that your
protein was unhappy in the restraints, of course. Perhaps you should
try some vacuum EM before you embed it in the lipid, or some such.
I'm using gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired
to be more gentle while releasing the restraint.Different
stepwise of releasing the restraint during NPT were tried and
followed by production MD, all the simulation stop or i shall
said it crashed around ~800ps with the same error (range
checking error). I'm out of idea what is the problem here.
Please advice.
Range checking is just one of many things that can be the first
thing to break when there's an underlying systemic problem.
Also, unless you need scientific continuity, 3.3.2 is about 4 years
old... 4.0.5 will be much faster!
Mark
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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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