[gmx-users] Error with equilibration of DPPC membrane with protein
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 30 13:22:26 CEST 2009
Edvin Erdtman wrote:
> 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
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
> 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.
> 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:
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.
> Thankful for all help we can get!
> /Edvin and Sujith
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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