[gmx-users] Lipid bilayer moved apart

Bing Bing jarbing09 at gmail.com
Sun Jun 28 12:27:41 CEST 2009

Dear All,
I'm simulating a empty membrane (128POPC + 2460 water) , the structure
obtained from Tielemen's website.
Thanks for the help from Justin and Mark, the structure had minimized and
stop at 217steps

Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
    5.20262e+03    1.01146e+04    4.17230e+03    3.36598e+03    7.50236e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    4.01104e+03    8.22333e+03   -1.49543e+04   -1.31978e+05   -1.41296e+05
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -2.52387e+05    0.00000e+00   -2.52387e+05    0.00000e+00    0.00000e+00

Steepest Descents converged to Fmax < 1000 in 217 steps
Potential Energy  = -2.52387473541938e+05
Maximum force     =  9.30404466610315e+02 on atom 5631
Norm of force     =  5.34591310731597e+03

The trajectory and energy seems ok.

With this, i proceed with NVT, although by looking at the energy and
temperature (300K) graph after NVT both looks fine. But when i tried to look
at the trajectory, i noticed that the upper layer lipid and lower layer
lapid actually moved further away from each other as compared to the
starting structure. And i don't know what cause this to happen. Please
Subsequently, i moved on with NPT and it stopped due to LINCS warning as

Step 269, time 0.538 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 1980 and 1981) rms inf
bonds that rotated more than 30 degrees:

This mean that some of the atoms in the structure is moving and it is out of
the cutt-off which being defined, it also said that it might due to the
reason that the starting structure is not equilibrated or many overlaps. But
as what i know,
the structure is well equilibrated. What is the reason for this? Is it
something which i missed out during NVT or NPT? Please advice.

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