Kirill Bessonov wrote:
Hello gain Justin,
Now I figured out that the problem was in gromacs version 4.0. So
peptide in water works no problem.
I have used trjconv -pbc mol -ur compact and it solved the artifact
problem. Thanks a lot!
Now I have started simulation on 96 CPU's for 1000ns total run time. But
after 1 day simulation the system crashed or exploded with the following
error: [First time it failed because of some problems with the server,
and then I have resumed the run using tpbconv -s DMPCRun1000ns.tpr -f
1000nsDMPCA141Run_part1.trr -extend 100000 -o DMPCRun100nspart2.tpr]
Which simulation? Peptide in water, or peptide-DMPC? This will be important
regarding the .mdp file you use.
Also, this use of tpbconv is obsolete. Use checkpoint files to obtain an exact
restart.
vol 0.78 imb F 2% pme/F 2.15 step 10578400, will finish Sat Aug 29
07:23:01 2009
vol 0.77 imb F 3% pme/F 2.15 step 10578500, will finish Sat Aug 29
07:28:32 2009
Step 10578599, time 21157.2 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.299801, max 6.073617 (between atoms 9449 and 9450)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
9451 9468 93.6 0.1530 0.1293 0.1530
Fatal error:
15 particles communicated to PME node 6 are more than a cell length out
of the domain decomposition cell of their charge group
I am attaching my mdp files used to to EM and MDrun here:
EM: http://kbessonov.googlepages.com/em_lipid.mdp MD:
http://kbessonov.googlepages.com/mdonly_1000ns.mdp
I was wondering why my system fails. and what can I do to avoid it? I
was thinking maybe to run several times EM on the system, maybe it will
help? What bugs me is that it fails really late in simulation. I have
not seen trajectory file yet.
I'm guessing this is for your lipid system (based on the em.mdp file name)?
What kind of equilibration are you using? Any position-restrained dynamics? If
you're not, then you probably should be :)
Any other comments are subject to knowing what system you're really dealing
with. If this is a peptide-membrane system, you'll need to make alterations to
your handling of COM motion removal, temperature coupling, and pressure coupling.
-Justin
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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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