Hi,
No obvious input issues are apparent from the information that
you provided, but there are a lot of unmentioned-ables, such as,
simulation system, prep protocol, etc.
See this long thread
http://archive.ambermd.org/201504/0213.html
where the ultimate resolution required attention to the details
of system preparation especially water models and ion parameters.
scott
On Wed, Oct 07, 2015 at 11:46:12PM +0000, Steven Cole Mercer wrote:
> Here is my minimization script:
> #!/bin/bash
> cat > mdin.in << EOF
> minimization
> &cntrl
> imin=1, ntpr=100, ntwx=100, maxcyc=10000,
> ntb=1,
> &end
> EOF
> # execute sander
> sander -O -i mdin.in -o min1.o -p hyd.parm7 -c hyd.rst7 -r min1.x -x min1.nc -e$
>
> And here is the following error that I am receiving:
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
> Backtrace for this error:
> #0 0x7FFEC5F882E7
> #1 0x7FFEC5F888EE
> #2 0x30E3E3269F
> #3 0x54DE60 in nb_adjust_
> #4 0x54FE2D in ewald_force_
> #5 0x700E42 in force_
> #6 0x4E6719 in runmin_
> #7 0x4D1579 in sander_
> #8 0x4C8408 in MAIN__ at multisander.F90:0
> ./runmin.sh: line 11: 28205 Segmentation fault sander -O -i mdin.in -o min1.o -p hyd.parm7 -c hyd.rst7 -r min1.x -x min1.nc -e min1.dat
>
> I can't find any of these errors so I'm not sure what is going wrong. All of my files are being referenced properly; can you shed some light on what might be happening?
>
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Received on Wed Oct 07 2015 - 18:00:03 PDT
