[gmx-users] .mdp file for polymer

[Mark Abraham]

varsha gautham wrote:
> Hello sir,
> 
> On giving gmxdump its giving me an error saying "segmentation fault.

99.9% of the time there is more information available. Check your 
stdout, stderr and the .log file.

>My 
> box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 50000 
> timesteps and with columb type=PME. I read from mailing list that PME 
> calculations requires large amount of memory space.Is this an issue with 
> dimension of box or with the system memory allocation ?Here's my log file.

You don't need/want PME for a system with only 106 atoms. A vacuum 
simulation also isn't likely to tell you anything useful.

> T-Coupling  :     106  (total 106 atoms)
> Energy Mon. :     106  (total 106 atoms)
> Acceleration:     106  (total 106 atoms)
> Freeze      :     106  (total 106 atoms)
> User1       :     106  (total 106 atoms)
> User2       :     106  (total 106 atoms)
> VCM         :     106  (total 106 atoms)
> XTC         :     106  (total 106 atoms)
> Or. Res. Fit:     106  (total 106 atoms)
> QMMM        :     106  (total 106 atoms)
> ben-nch0.xtc frame 0:
>    natoms=         1  step=         0  time=-2.9120485e-05  prec=2.8026e-45
>    box (3x3):
>       box[    0]={-2.89059e-05,  3.98821e-34, -2.39380e-05}
>       box[    1]={ 3.98770e-34,  1.40130e-45, -2.91168e-05}
>       box[    2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
>    x (1x3):
> Segmentation fault
>  
> 
> 
> 
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