you'll need to give more details, we don't know anything about your system.
On Thu, Jun 28, 2012 at 3:43 PM, Wilson, Katie <ka.wilson.uleth.ca> wrote:
> I actually did used the image command before calcuating the rmsd and it
> didnt seem to make a difference. I used
>
> trajin md2.mdcrd 1 50000 10
> trajout strip.mdcrd
> center :1-354 mass origin
> image origin center
> rms first out rms.out .CA,C,N
>
> Katie
>
> > is it possible you're calculating the rmsd for a group that involves more
> > than 1 molecule? if yes, loko in the archives and the manual for the
> image
> > command.
> >
> > On Thu, Jun 28, 2012 at 3:22 PM, Wilson, Katie <ka.wilson.uleth.ca>
> wrote:
> >
> >> Hello,
> >> When I calculate the rmsd value with ptraj on AMBER 11 (rms first out
> >> rms
> >> .CA,C,N) the value jumps from 2 to 25 and then 25 to 500. What would
> >> cause
> >> these jumps to occur and how do I fix the rmsd calculation so these
> >> jumps
> >> do not occur?
> >> Thanks,
> >> Katie
> >>
> >>
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> >>
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> >
>
>
>
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Received on Thu Jun 28 2012 - 13:00:04 PDT
