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