On Mon, Aug 16, 2010 at 9:00 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi,
>
> Removing the go from the file solved the problem - perfect! Why I do not
> quite understand.....
>
> Why does VMD keep the bond between the two hydrogens in the water
> molecules?
>
Because I believe that's how it's defined in the TIP3P water model, and
therefore that's the bond information that's stored in the prmtop. VMD
displays bonds present in the prmtop file.
Hope this helps,
Jason
>
> On Mon, Aug 16, 2010 at 2:18 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > 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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> > >
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 16 2010 - 06:30:09 PDT
