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?
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?
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.
<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
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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