Hi
I am want to re-image my simulation but I get the segmentation fault from
the simulation. My complex is rather big so I wonder if this is the problem
or if the issue is my simulation data?
My input file is
trajin md_0_5.mdcrd
trajout md_0_5_re_image.mdcrd
center :1-1000
image familiar
go
where the 1-1000 are protein atoms when I execute the script
ptraj protein_solv.prmtop < re_image_traj.ptraj
it runs through
PTRAJ: go
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 125 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (md_0_5.mdcrd) is an AMBER trajectory (with box info) with 125 sets
OUTPUT COORDINATE FILE
File (md_0_5_re_image.mdcrd) is an AMBER trajectory (with box info)
ACTIONS
1> IMAGE familiar by molecule to box center using the first atom, atom
selection * (All atoms are selected)
IMAGE familiar, center is at box center
Processing AMBER trajectory file md_0_5.mdcrd
Set 1 .................................................
Set 50 .................................................
Set 100 .........................Segmentation fault
How to fix this - more memory or ?
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Received on Mon Aug 16 2010 - 01:30:03 PDT
