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

Kirill Bessonov kbessonov at gmail.com
Thu Jul 16 22:29:00 CEST 2009

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?

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

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

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.

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?

Could you explain from your tutorial:

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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090716/f0295c1c/attachment.html>

More information about the gromacs.org_gmx-users mailing list