[gmx-users] DPPC/DPPE/H2O simulation

Sukit Leekumjorn leekumjo at vt.edu
Wed Mar 2 04:22:25 CET 2005

Dear GMX Users,

This is my first time using Gromacs and I came across a problem while 
running the simulation.

Right now I have a properly working DPPC/water system and I am trying to 
modify it.  My task is to substitute some of the DPPC with DPPE 
molecules (very much the same in structure except CH3 is replaced by H 
on the amine group).  I did the following:
1)    change the molecules CH3 to H in the .gro file
2)    add an H in the ff parameter so that all of the parameters are listed
3)    add another line in ff...nb LJ of C6=0 and C12=0 for hydrogen

The problem come when running this system.  It look like the H on the 
amine group is trying to hydrogen bond with the the Oxygen in the 
phosphate group and breaking all the bonds (error pdb file viewed using 
VMD).  I tried running at a smaller stepsize in the double precision 
mode and  it gave me the same problem.  Here is the error:

relative constraint deviation after LINCS:
max 0.012353 (between atoms 3 and 4) rms 0.001894
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
     3      4   69.9    0.1010   0.0988      0.1000

Despite these errors, I did use different LJ parameters for hydrogen 
(C6=0.00001e-2 and C12=0.00001e-4) and the simulation runs without 
giving any error (2ps run).  This I hope to equilibrate the system first 
due to switching the CH3 with H molecules.  Then I  convert LJ 
parameters back to  zeros and run the simulation again with the same 
errors listed above.

If anyone came across this problem with your DPPE or POPE (same 
headgroup) in the past and solved this problem, any help in this matter 
would be greatly appreciated.

Sukit Leekumjorn

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