How many atoms are in your system? I can't reproduce this problem with
a 1000 frame trajectory of 49115 atoms.
It seems from your ptraj output that you are using an earlier version
of ptraj (<AT 1.4). Is this the case? If so, upgrading to ptraj from
AT 1.4 may work.
Here's something else to try that is a long shot but has worked for me
with previous versions of ptraj. I notice that you are passing your
input file in as STDIN. Does the segfault occur if you remove the 'go'
from the input file and pass it to ptraj as an argument instead? E.g.:
modified ptraj.in:
trajin md_0_5.mdcrd
trajout md_0_5_re_image.mdcrd
center :1-1000
image familiar
execute with:
ptraj PRMTOP ptraj.in
-Dan
On Mon, Aug 16, 2010 at 4:01 AM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 16 2010 - 05:30:03 PDT
