[gmx-users] Re: Error in Membrane simulations with POPC bilayer

[Justin A. Lemkul]

On 7/12/12 4:59 AM, J Peterson wrote:
> Hi Justin,
>
> Thanks for the effort to help me.
>
> I still no out of the error. The following is the content of my
> topol_popc.top
>
> ; Include chain topologies
> #include "gromos53a6_lipid.ff/forcefield.itp"
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> ; Include ion topologies
> #include "gromos53a6_lipid.ff/ions.itp"
>
> ; System specifications
> [ system ]
> 128-Lipid POPC Bilayer
>
> [ molecules ]
> ; molecule name nr.
> POPC 128
> SOL 2460
>
> And the following is the first part of my popc128b.gro file
>
> Alm on surf + relaxed popc
> 14036
>      1POP     C1    1   0.253   5.425   1.688
>      1POP     C2    2   0.428   5.314   1.792
>      1POP     C3    3   0.334   5.243   1.571
>      1POP     N4    4   0.378   5.352   1.660
>      1POP     C5    5   0.474   5.439   1.590
>      1POP     C6    6   0.606   5.390   1.531
>      1POP     O7    7   0.692   5.366   1.643
>      1POP     P8    8   0.834   5.316   1.587
>      1POP     O9    9   0.800   5.197   1.505
>      1POP    O10   10   0.903   5.435   1.533
>      1POP    O11   11   0.890   5.266   1.729
>      1POP    C12   12   0.823   5.142   1.753
>      1POP    C13   13   0.836   5.086   1.895
>      1POP    O14   14   0.766   4.964   1.924
>      1POP    C15   15   0.632   4.959   1.944
>      1POP    O16   16   0.555   5.019   1.869
>      1POP    C17   17   0.589   4.833   2.020
>      1POP    C18   18   0.615   4.703   1.944
>      1POP    C19   19   0.595   4.575   2.025
>      1POP    C20   20   0.625   4.467   1.920
>      1POP    C21   21   0.677   4.340   1.987
>      1POP    C22   22   0.813   4.357   2.055
>      1POP    C23   23   0.848   4.223   2.120
>      1POP    C24   24   0.884   4.121   2.012
>      1POP    C25   25   0.957   4.013   2.043
>      1POP    C26   26   0.994   3.986   2.189
>      1POP    C27   27   1.069   3.853   2.202
>      1POP    C28   28   0.967   3.739   2.204
>      1POP    C29   29   1.012   3.593   2.202
>      1POP    C30   30   0.916   3.478   2.169
>      1POP    C31   31   0.869   3.518   2.029
>      1POP    C32   32   0.801   5.205   1.983
> .
> .
> .
> .
> .
>
> What are the parts mismatching in these files?

 From what's shown, it's impossible to tell.  Based on this information, 
everything lines up.  I'm assuming the original coordinate file and the popc.itp 
topology came from Tieleman's site?

> Since it says the atom names from the top file will be used, is it safe to
> ignore this warning too?
>

No.  The naming mismatches imply that grompp is trying to map parameters for 
lipids onto water molecules.  The resulting simulation will be nonsense and will 
probably crash immediately.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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