[gmx-users] Energy Minimization with Lipid Bilayer

[Justin Lemkul]

> 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
output:

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
md.log:

            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?

Thanks,
Justin