Hi again an Thank you for comments!
Justin A. Lemkul wrote:
Edvin Erdtman wrote:
Hi
We have a problem of equilibrate the system with a protein within
DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have
been using their perl script inflategro.pl to insert our protein. We
used position restraints for the protein as mentioned in Methods 41
(2007) 475-488.
We have tried with a scaling factor of 0,95 and 0,97, and a cut-off
value of 14 to expand the box and 0 to reduce the box (is that ok???).
perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5
em2/area.dat
with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps
were followed.
This seems reasonable.
When we have not used position restraints for the protein, and used a
cutoff value of 4 Å, the simulation were performed well even without
annealing.
4 A cutoff? For what? That is far too short for a lipid bilayer
simulation. Or am I misunderstanding where you are applying this 4 A?
Is it part of InflateGRO?
Yes that is a cut-off for the InflateGRO. cutoff of distance between
alpha-carbon of protein and phosphorus atoms in DPPC (0 in the upper
example of running the perl script). If the distance are within this
value, then that DPPC will be removed. I thought that this parameter was
used only in the diverging step with Inflategro, not when compressing
the system. Therefore we tried to run calculations with that parameter
set to 0 instead (above).
We have tried to energy minimize the system with steepest descent
method in each step of decreasing the box.
Do each of these minimizations complete satisfactorily?
Most of them converged to Fmax < 1000.
After water soaking, we have tried with both cg and steep energy
minimizations.
The problems we are facing:
- All the energy minimizations are not reaching Fmax < 1000
How close to Fmax are you getting? If it's still on the order of 10^3
you may be OK; if it's a lot larger then you have other problems to
deal with.
The highest force we got (using scaling factor = 0.97) at step 33:
"Maximum force = 2.6218958e+03 on atom 4591"
<snip>
tcoupl = Nose-hoover
tc-grps = DPPC Cl SOL Protein
tau_t = 0.1 0.1 0.1 0.1
ref_t = 100 100 100 100
Here is a potential problem. Never couple solvent and ions
separately. Make an index group of these two merged species. See here:
http://wiki.gromacs.org/index.php/thermostats
Thank you for that advice, I will do that. But really I don't think that
is our main problem. We tried also without chlorine (system total charge
of +2), but we got the same error.
Another bit of general advice. I had a very mysterious problem once
where during equilibration of a DPPC bilayer my lipids were blowing
apart for no apparent reason. Upon very close inspection of the
trajectory (setting nstxout = 1) I identified the initial location of
the explosion. A Cl- ion was immediately next to a phosphate oxygen
(very hard to see!), and it was causing a huge force that was ripping
my lipid apart.
Just an idea, if the InflateGRO minimizations are working OK, but the
solvated system with ions is not working.
-Justin
Thankful for all help we can get!
/Edvin and Sujith
/Edvin
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