[gmx-users] Energy Minimization with Lipid Bilayer

[Justin Lemkul]

Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:

> Justin Lemkul wrote:
>
> > I also tried running a position-restrained MD (just to see if it might give
> me
> > something different), holding the DPPC bilayer fixed and allowing the
> solvent
> > to move, but I was again frustrated to see:
> >
> > 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.
> >
> > In the MD, I am applying PBC.  I am wondering if this output is a result of
> a
> > poorly minimized starting structure, or if these errors are in any way
> related?
>
> Hmmm in order that we can see what your .gro file is doing, can you
> please post the results of
>
> head -n 10 conf.gro
> tail -n 10 conf.gro
> wc -l conf.gro

Hopefully this will help:

$ head -n 10 conf.gro

Box of water, 7996 residues
30388
    1DPPC    C1    1   1.513   5.763   5.082
    1DPPC    C2    2   1.563   5.543   5.152
    1DPPC    C3    3   1.523   5.723   5.312
    1DPPC    N4    4   1.583   5.683   5.182
    1DPPC    C5    5   1.723   5.723   5.172
    1DPPC    C6    6   1.833   5.663   5.272
    1DPPC    O7    7   1.863   5.523   5.252
    1DPPC    P8    8    2.003   5.503   5.332

$ tail -n 10 conf.gro

 8122SOL     OW30380   5.867   9.576   5.792
 8122SOL    HW130381   5.945   9.624   5.752
 8122SOL    HW230382   5.897   9.515   5.862
 8123SOL     OW30383   0.282   9.624   5.672
 8123SOL    HW130384   0.319   9.615   5.582
 8123SOL    HW230385   0.345   9.580   5.742
 8124SOL     OW30386   5.624   9.670   5.872
 8124SOL    HW130387   5.609   9.766   5.852
 8124SOL    HW230388   5.715   9.641   5.842
   6.25000  10.69300   6.25000

$ wc -l conf.gro

 30391 conf.gro

Thanks,
Justin