[gmx-users] Peptide - DMPC membrane simulations -> Unstable system

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 16 22:39:49 CEST 2009

Kirill Bessonov wrote:
> Thank you Justin,
> I have tried to just solvate the peptide in water box using genbox 
> command and spc216 water
> Then I have used the Energy Min mdp file form your tutorial (I have been 
> folowing your tutorial for couple of days, the difference is that I want 
> to put my segment on top of the membrane between the head groups of 
> phospholipids). The DMPC box is stable, but I have trouble with 14aa 
> peptide. It seems that is is unstable, I have made NH2 and COOO termini, 
> maybe this is the problem?

So, to clarify, you are embedding a peptide within the headgroups of a bilayer, 
not diffusing in water above the bilayer?  What method are you using to delete 
overlapping lipids?  InflateGRO?

Setting those termini should not be the problem, in and of itself.

> The results of EM for peptide in water:
> Step=  786, Dmax= 6.3e-03 nm, Epot= -1.37798e+06 Fmax= 7.60491e+02, atom= 67
> writing lowest energy coordinates.
> Steepest Descents converged to Fmax < 1000 in 787 steps
> Potential Energy  = -1.3779814e+06
> Maximum force     =  7.6049121e+02 on atom 67
> Norm of force     =  1.8584177e+01

That all looks quite good.

> Then I run mdrun using mdp file that we use usually in our lab, and 
> system crashed with LINCS warnings after 75 steps.

Can you post that .mdp file?

> But when I use the mdp file that is in EM section of your tutorial and 
> change integrator = md. The peptide in water system is running without 
> any warnings up till step 300.

Don't.  That file is for EM, with every other setting at default, which, IIRC, 
will not be appropriate for running MD.

> step 300, Warning: 1-4 interaction between 54 and 59 at distance 2.342 
> which is larger than the 1-4 table size 2.200 nm
> What settings would you recommend for MD runs in mdp files?

Many settings depend on the force field model chosen.  I can't make such a 
generic recommendation.

Are you applying any position restraints to the protein to allow the lipids to 
pack around it?  If you have voids around your lipid head groups, are you 
applying position restraints to the lipid head groups to allow water to soak in?

Have you watched the output trajectory to see where things are falling apart?

> Could you explain from your tutorial:

Note that the following comments are intended when there are voids around the 
lipid headgroups, or you specifically note that headgroups are collapsing in on 
themselves for specific lipids like POPE and POPG.  They are not a generic 
solution for LINCS problems or other system collapses.

Just a disclaimer for the archive :)

> How to Reduce the charges on the H atoms (all the way to zero, if 
> necessary) Restore the charges before continuing

Set the charge = 0.000 for H atoms in the lipid topology.  This should not 
affect you; DMPC should not hydrogen bond within itself.

> And how Add [ exclusions ] within the topology between H and phosphate O 
> atoms Remove the exclusions before continuing

Make an [ exclusions ] directive and enter the atom numbers of the corresponding 
atoms.  Chapter 5 is your friend here.  Also not likely to be useful in your 
case, for the same reason above.


> Thanks
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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


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