[gmx-users] Re: Regarding POPE " H " atom type modification

[Oliver Mirus]

Hi,

> In both the cases i got the error as show below.
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 2095.427979 (between atoms 4422 and 4424) rms
> 69.822533
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>       1      4   90.0    0.1000   3.5921      0.1000
>       2      4   90.0    0.1000  29.8166      0.1000
>       3      4   90.0    0.1000   3.4683      0.1000
>       4      5   90.0    0.1470   3.7039      0.1470
>       5      6   67.6    0.1530   0.1440      0.1530
>       6      7   90.2    0.1430   1.8286      0.1430
>       7      8   90.0    0.1610   1.2737      0.1610
> ....................
> ...................
> ...................
> after some time segmentation fault
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx\
> Could you suggest me where I have done mistake.

check your system carefully. Maybe insufficient energy minimization? 
Don't forget to use position restrained MD to relax the system prior to 
your production MD run.
I have had no troubles with this POPC system from Dr. Tieleman's website:
http://moose.bio.ucalgary.ca/files/popc128b.pdb

Also, check out the talk on "Membrane simulations" from the Gromacs 
Workshop 2007:
http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007

regards

Oliver