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 <[EMAIL PROTECTED]> 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
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