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

[J Peterson]

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

Thanks,

Peterson J

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