[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:
> 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.


> 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
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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