[gmx-users] Lipid bilayer moved apart
jarbing09 at gmail.com
Sun Jun 28 12:27:41 CEST 2009
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
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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