Greetings,
Could you perhaps provide details of your energy minimization
(conjugated? steep? etc.) and perhaps your mdp file for the simulation
as well.
What kind of pressure couplings did you use? (isotropic? semi-isotropic? etc.)
How much further away did each layer move?
I think it is usually recommended to simulate membranes with
semi-isotropic pressure coupling, though I am not sure what is the
cause of the error you are getting with NPT and LINCS.
Regards,
-Shay
Quoting "Bing Bing" <jarbin...@gmail.com>:
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
advice.
Subsequently, i moved on with NPT and it stopped due to LINCS warning as
below:-
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.
Regards,
Bing
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