[gmx-users] segmentation fault

[Tsjerk Wassenaar]

Hi Priya,

What is the rationale for decreasing box dimensions, if it explodes?
First of all, does your peptide fit in a box with dimensions 0.9 nm?
And what about your cut-off length? I would think that with such a
small box, your peptide overlaps with its own periodic images, giving
a good recipe for a crash as you observed.

Check your input...

Best,

Tsjerk

On 2/27/07, priya priya <priyaanand_27 at yahoo.co.in> wrote:
> Dear All
>  I am facing a problem in gromacs............after running MD in water for a
>  a linear peptide
>  steps i did...
>  1. created a box of dimensions 0.9nm , added water molecules
>  2. did energy minimization
>  3. Position rest MD for 20ns
>  4. Production MD for 1ns
>  But it ends with segmentation fault.....while checking the log file it
> showed that box exploded........so i again started the run by decreasing the
> box dimensions to 0.85nm. systen is again showing segmentation fault but no
> information is specified in the log file.
>  Please guide.
>
>  Thanks in advance
>  Priya
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623