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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Received on Thu Jun 28 2012 - 13:00:03 PDT
