What do you mean by more complex script. As I took a look at the archives
and didn't seem to find any rmsd scripts for systems with multiple
molecules.
> it sounds like you have 3 molecules, so you'd need a more complex script
> than this. take a look through the archives for examples.
>
> On Thu, Jun 28, 2012 at 3:52 PM, Wilson, Katie <ka.wilson.uleth.ca> wrote:
>
>> My system is a DNA-protein complex which I have run 10 ns of production
>> MD
>> without restraints with constant pressure and temperature and with PBC.
>> I
>> am trying to calculate rmsd based on the protein's backbone and center
>> it
>> based on the protein resdides (resdiues 1-354).
>>
>> > 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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>> >
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>>
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Received on Thu Jun 28 2012 - 14:30:03 PDT
