[gmx-users] Energy Minimization with Lipid Bilayer

Justin Lemkul jalemkul at vt.edu
Wed Nov 22 01:47:51 CET 2006

> Hallo!
> As you mentioned before you are not using PBC. However, if the membrane
> in the box was equilibrated using PBC then it might be that some residues
> are "cut in a half". So perhaps take a look at your Lipids and make sure that
> all parts of a phospholipid molecule are on the same side of the box.
> Just a thought, might be pointless.

Any application of PBC gives me a scrambled structure, with my system divided in
half through the y-axis within the box.  If I attempt position-restrained MD
(keeping the bilayer fixed, allowing solvent to relax), I get the following

Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.

If I remove position restraints, I get similar results, such as this, from my

            Step           Time         Lambda
            750        1.50000        0.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.000000      1      4   nan
        After LINCS         0.000000      1      4   nan

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
            nan            nan            nan            nan            nan
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
            nan            nan            nan            nan            nan
   Total Energy    Temperature Pressure (bar)
            nan            nan            nan

Does this provide any clues as to what might be going on?


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